Package: guix-patches;
Reported by: zimoun <zimon.toutoune <at> gmail.com>
Date: Fri, 21 May 2021 20:23:01 UTC
Severity: normal
Tags: patch
Done: Ricardo Wurmus <rekado <at> elephly.net>
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rekado <at> elephly.net, guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:23:01 GMT) Full text and rfc822 format available.zimoun <zimon.toutoune <at> gmail.com>:rekado <at> elephly.net, guix-patches <at> gnu.org.
(Fri, 21 May 2021 20:23:01 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: guix-patches <at> gnu.org Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:21:36 +0200
Hi,
Janitor [1] patch set. It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor).
1: <https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html>
To transfer the Copyright, I use:
git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r-<name>
I did my best to preserve the copyright. But I do not guarantee it is error-free.
Well, in doubt, I have been conservative.
Then, I do:
guix build r-<name> --no-grafts
./pre-inst-env guix build r-<name> --no-grafts --check
To avoid a break, I check with:
for ci in $(git log --format="%H" -51 --reverse);
do
./pre-inst-env guix pull --commit=$ci \
-p /tmp/test-${ci} \
--url=$(pwd) --branch=janitor --disable-authentication
done
and everyting seems fine. At least, "guix pull" should be checked at the end
of the series.
Last, I have checked the imported modules in gnu/packages/bioinformatics.scm.
All should be fine.
Now, I get:
--8<---------------cut here---------------start------------->8---
$ ag 'bioconductor' gnu/packages/bioinformatics.scm
69: #:use-module (gnu packages bioconductor)
11550: (synopsis "Extra base functions for Bioconductor")
11553:provided by Bioconductor packages.")
--8<---------------cut here---------------end--------------->8---
which ends the move, I guess. Except the package r-rcurl in
gnu/packages/statistics.scm, let as an exercise for the reader. ;-)
On a side note about the Copyright lines, I did:
git blame --date=format:"%Y)" gnu/packages/bioinformatics.scm \
| cut -d')' -f1 | cut -d'(' -f2 | sed 's/ //g' \
| sort | uniq -c
and it is possible that there is some "mistake", FWIW.
All the best,
simon
zimoun (50):
gnu: r-genomicalignments: Move to (gnu packages bioconductor).
gnu: r-rtracklayer: Move to (gnu packages bioconductor).
gnu: r-genomicfeatures: Move to (gnu packages bioconductor).
gnu: r-topgo: Move to (gnu packages bioconductor).
gnu: r-bsgenome: Move to (gnu packages bioconductor).
gnu: r-msnid: Move to (gnu packages bioconductor).
gnu: r-msnbase: Move to (gnu packages bioconductor).
gnu: r-samr: Move to (gnu packages bioconductor).
gnu: r-impute: Move to (gnu packages bioconductor).
gnu: r-seqpattern: Move to (gnu packages bioconductor).
gnu: r-go-db: Move to (gnu packages bioconductor).
gnu: r-genomation: Move to (gnu packages bioconductor).
gnu: r-genomationdata: Move to (gnu packages bioconductor).
gnu: r-pcamethods: Move to (gnu packages bioconductor).
gnu: r-mzid: Move to (gnu packages bioconductor).
gnu: r-aroma-light: Move to (gnu packages bioconductor).
gnu: r-deseq: Move to (gnu packages bioconductor).
gnu: r-edaseq: Move to (gnu packages bioconductor).
gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor).
gnu: r-annotationhub: Move to (gnu packages bioconductor).
gnu: r-fastseg: Move to (gnu packages bioconductor).
gnu: r-affy: Move to (gnu packages bioconductor).
gnu: r-keggrest: Move to (gnu packages bioconductor).
gnu: r-gage: Move to (gnu packages bioconductor).
gnu: r-complexheatmap: Move to (gnu packages bioconductor).
gnu: r-genomicfiles: Move to (gnu packages bioconductor).
gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor).
gnu: r-organismdbi: Move to (gnu packages bioconductor).
gnu: r-affyio: Move to (gnu packages bioconductor).
gnu: r-vsn: Move to (gnu packages bioconductor).
gnu: r-biovizbase: Move to (gnu packages bioconductor).
gnu: r-ensembldb: Move to (gnu packages bioconductor).
gnu: r-mzr: Move to (gnu packages bioconductor).
gnu: r-protgenerics: Move to (gnu packages bioconductor).
gnu: r-sva: Move to (gnu packages bioconductor).
gnu: r-motifrg: Move to (gnu packages bioconductor).
gnu: r-seqlogo: Move to (gnu packages bioconductor).
gnu: r-zlibbioc: Move to (gnu packages bioconductor).
gnu: r-rhtslib: Move to (gnu packages bioconductor).
gnu: r-bamsignals: Move to (gnu packages bioconductor).
gnu: r-rcas: Move to (gnu packages bioconductor).
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).
gnu: r-tximport: Move to (gnu packages bioconductor).
gnu: r-rhdf5filters: Move to (gnu packages bioconductor).
gnu: r-annotationfilter: Move to (gnu packages bioconductor).
gnu: r-rhdf5: Move to (gnu packages bioconductor).
gnu: r-chipseq: Move to (gnu packages bioconductor).
gnu: r-copyhelper: Move to (gnu packages bioconductor).
gnu: r-copywriter: Move to (gnu packages bioconductor).
gnu: r-methylkit: Move to (gnu packages bioconductor).
gnu/packages/bioconductor.scm | 1826 +++++++++++++++++++++++++++++--
gnu/packages/bioinformatics.scm | 1645 ----------------------------
gnu/packages/cran.scm | 30 -
3 files changed, 1749 insertions(+), 1752 deletions(-)
base-commit: bd382fae71d899e243e81688bf5baed26171f2ea
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:27:02 GMT) Full text and rfc822 format available.Message #8 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 02/50] gnu: r-rtracklayer: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:34 +0200
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
---
gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 48 ---------------------------------
2 files changed, 48 insertions(+), 48 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4f4ff82ad0..42a3d1fffc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2385,6 +2385,54 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
tab-delimited (tabix) files.")
(license license:expat)))
+(define-public r-rtracklayer
+ (package
+ (name "r-rtracklayer")
+ (version "1.50.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rtracklayer" version))
+ (sha256
+ (base32
+ "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-zlib
+ (lambda _
+ (substitute* "DESCRIPTION"
+ ((" zlibbioc,") ""))
+ (substitute* "NAMESPACE"
+ (("import\\(zlibbioc\\)") ""))
+ #t)))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/rtracklayer")
+ (synopsis "R interface to genome browsers and their annotation tracks")
+ (description
+ "rtracklayer is an extensible framework for interacting with multiple
+genome browsers (currently UCSC built-in) and manipulating annotation tracks
+in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
+built-in). The user may export/import tracks to/from the supported browsers,
+as well as query and modify the browser state, such as the current viewport.")
+ (license license:artistic2.0)))
+
(define-public r-shortread
(package
(name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d0fe1df30..9fb46c0d5d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-rtracklayer
- (package
- (name "r-rtracklayer")
- (version "1.50.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "rtracklayer" version))
- (sha256
- (base32
- "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'use-system-zlib
- (lambda _
- (substitute* "DESCRIPTION"
- ((" zlibbioc,") ""))
- (substitute* "NAMESPACE"
- (("import\\(zlibbioc\\)") ""))
- #t)))))
- (native-inputs
- `(("pkg-config" ,pkg-config)))
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xml" ,r-xml)
- ("r-xvector" ,r-xvector)
- ("r-zlibbioc" ,r-zlibbioc)))
- (home-page "https://bioconductor.org/packages/rtracklayer")
- (synopsis "R interface to genome browsers and their annotation tracks")
- (description
- "rtracklayer is an extensible framework for interacting with multiple
-genome browsers (currently UCSC built-in) and manipulating annotation tracks
-in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
-built-in). The user may export/import tracks to/from the supported browsers,
-as well as query and modify the browser state, such as the current viewport.")
- (license license:artistic2.0)))
-
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:27:02 GMT) Full text and rfc822 format available.Message #11 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 01/50] gnu: r-genomicalignments: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:33 +0200
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
---
gnu/packages/bioconductor.scm | 35 ++++++++++++++++++++++++++++++++-
gnu/packages/bioinformatics.scm | 33 -------------------------------
2 files changed, 34 insertions(+), 34 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 45e31a5760..4f4ff82ad0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado <at> elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado <at> elephly.net>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel <at> gnu.org>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix <at> thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben <at> gmail.com>
@@ -2075,6 +2075,39 @@ translation between different chromosome sequence naming conventions (e.g.,
names in their natural, rather than lexicographic, order.")
(license license:artistic2.0)))
+(define-public r-genomicalignments
+ (package
+ (name "r-genomicalignments")
+ (version "1.26.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicAlignments" version))
+ (sha256
+ (base32
+ "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
+ (properties
+ `((upstream-name . "GenomicAlignments")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/GenomicAlignments")
+ (synopsis "Representation and manipulation of short genomic alignments")
+ (description
+ "This package provides efficient containers for storing and manipulating
+short genomic alignments (typically obtained by aligning short reads to a
+reference genome). This includes read counting, computing the coverage,
+junction detection, and working with the nucleotide content of the
+alignments.")
+ (license license:artistic2.0)))
+
(define-public r-genomicranges
(package
(name "r-genomicranges")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9c77d66a35..0d0fe1df30 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,39 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-genomicalignments
- (package
- (name "r-genomicalignments")
- (version "1.26.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomicAlignments" version))
- (sha256
- (base32
- "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
- (properties
- `((upstream-name . "GenomicAlignments")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (home-page "https://bioconductor.org/packages/GenomicAlignments")
- (synopsis "Representation and manipulation of short genomic alignments")
- (description
- "This package provides efficient containers for storing and manipulating
-short genomic alignments (typically obtained by aligning short reads to a
-reference genome). This includes read counting, computing the coverage,
-junction detection, and working with the nucleotide content of the
-alignments.")
- (license license:artistic2.0)))
-
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:27:03 GMT) Full text and rfc822 format available.Message #14 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 03/50] gnu: r-genomicfeatures: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:35 +0200
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 43 ---------------------------------
2 files changed, 43 insertions(+), 43 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 42a3d1fffc..2263c17cc4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2108,6 +2108,49 @@ junction detection, and working with the nucleotide content of the
alignments.")
(license license:artistic2.0)))
+(define-public r-genomicfeatures
+ (package
+ (name "r-genomicfeatures")
+ (version "1.42.3")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicFeatures" version))
+ (sha256
+ (base32
+ "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
+ (properties
+ `((upstream-name . "GenomicFeatures")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/GenomicFeatures")
+ (synopsis "Tools for working with transcript centric annotations")
+ (description
+ "This package provides a set of tools and methods for making and
+manipulating transcript centric annotations. With these tools the user can
+easily download the genomic locations of the transcripts, exons and cds of a
+given organism, from either the UCSC Genome Browser or a BioMart
+database (more sources will be supported in the future). This information is
+then stored in a local database that keeps track of the relationship between
+transcripts, exons, cds and genes. Flexible methods are provided for
+extracting the desired features in a convenient format.")
+ (license license:artistic2.0)))
+
(define-public r-genomicranges
(package
(name "r-genomicranges")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9fb46c0d5d..bf8cb2f3a5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,49 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-genomicfeatures
- (package
- (name "r-genomicfeatures")
- (version "1.42.3")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomicFeatures" version))
- (sha256
- (base32
- "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
- (properties
- `((upstream-name . "GenomicFeatures")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-dbi" ,r-dbi)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/GenomicFeatures")
- (synopsis "Tools for working with transcript centric annotations")
- (description
- "This package provides a set of tools and methods for making and
-manipulating transcript centric annotations. With these tools the user can
-easily download the genomic locations of the transcripts, exons and cds of a
-given organism, from either the UCSC Genome Browser or a BioMart
-database (more sources will be supported in the future). This information is
-then stored in a local database that keeps track of the relationship between
-transcripts, exons, cds and genes. Flexible methods are provided for
-extracting the desired features in a convenient format.")
- (license license:artistic2.0)))
-
(define-public r-go-db
(package
(name "r-go-db")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:02 GMT) Full text and rfc822 format available.Message #17 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 06/50] gnu: r-msnid: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:38 +0200
* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
---
gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 52 ---------------------------------
2 files changed, 52 insertions(+), 52 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 923413135b..b5787cb207 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2312,6 +2312,58 @@ and the assessment of differential expression. The analysis methods apply to
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
+(define-public r-msnid
+ (package
+ (name "r-msnid")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MSnID" version))
+ (sha256
+ (base32
+ "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
+ (properties `((upstream-name . "MSnID")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationhub" ,r-annotationhub)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocstyle" ,r-biocstyle)
+ ("r-biostrings" ,r-biostrings)
+ ("r-data-table" ,r-data-table)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dplyr" ,r-dplyr)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iterators" ,r-iterators)
+ ("r-msnbase" ,r-msnbase)
+ ("r-msmstests" ,r-msmstests)
+ ("r-mzid" ,r-mzid)
+ ("r-mzr" ,r-mzr)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-purrr" ,r-purrr)
+ ("r-r-cache" ,r-r-cache)
+ ("r-rcpp" ,r-rcpp)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rlang" ,r-rlang)
+ ("r-runit" ,r-runit)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-xtable" ,r-xtable)))
+ (home-page "https://bioconductor.org/packages/MSnID")
+ (synopsis "Utilities for LC-MSn proteomics identifications")
+ (description
+ "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
+from mzIdentML (leveraging the mzID package) or text files. After collating
+the search results from multiple datasets it assesses their identification
+quality and optimize filtering criteria to achieve the maximum number of
+identifications while not exceeding a specified false discovery rate. It also
+contains a number of utilities to explore the MS/MS results and assess missed
+and irregular enzymatic cleavages, mass measurement accuracy, etc.")
+ (license license:artistic2.0)))
+
(define-public r-rbgl
(package
(name "r-rbgl")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9c9288c6b0..5c2abe6e94 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9275,58 +9275,6 @@ structure (pcaRes) to provide a common interface to the PCA results.")
of mass spectrometry based proteomics data.")
(license license:artistic2.0)))
-(define-public r-msnid
- (package
- (name "r-msnid")
- (version "1.24.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "MSnID" version))
- (sha256
- (base32
- "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
- (properties `((upstream-name . "MSnID")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationhub" ,r-annotationhub)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocstyle" ,r-biocstyle)
- ("r-biostrings" ,r-biostrings)
- ("r-data-table" ,r-data-table)
- ("r-doparallel" ,r-doparallel)
- ("r-dplyr" ,r-dplyr)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iterators" ,r-iterators)
- ("r-msnbase" ,r-msnbase)
- ("r-msmstests" ,r-msmstests)
- ("r-mzid" ,r-mzid)
- ("r-mzr" ,r-mzr)
- ("r-protgenerics" ,r-protgenerics)
- ("r-purrr" ,r-purrr)
- ("r-r-cache" ,r-r-cache)
- ("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
- ("r-rlang" ,r-rlang)
- ("r-runit" ,r-runit)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-xtable" ,r-xtable)))
- (home-page "https://bioconductor.org/packages/MSnID")
- (synopsis "Utilities for LC-MSn proteomics identifications")
- (description
- "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
-from mzIdentML (leveraging the mzID package) or text files. After collating
-the search results from multiple datasets it assesses their identification
-quality and optimize filtering criteria to achieve the maximum number of
-identifications while not exceeding a specified false discovery rate. It also
-contains a number of utilities to explore the MS/MS results and assess missed
-and irregular enzymatic cleavages, mass measurement accuracy, etc.")
- (license license:artistic2.0)))
-
(define-public r-aroma-light
(package
(name "r-aroma-light")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:02 GMT) Full text and rfc822 format available.Message #20 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 05/50] gnu: r-bsgenome: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:37 +0200
* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
---
gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++-
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2afb5214ee..923413135b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
;;; Copyright © 2016 Pjotr Prins <pjotr.guix <at> thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben <at> gmail.com>
;;; Copyright © 2017 Efraim Flashner <efraim <at> flashner.co.il>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me <at> tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me <at> tobias.gr>
;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau <at> gmail.com>
;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
@@ -1875,6 +1875,37 @@ matching algorithms, and other utilities, for fast manipulation of large
biological sequences or sets of sequences.")
(license license:artistic2.0)))
+(define-public r-bsgenome
+ (package
+ (name "r-bsgenome")
+ (version "1.58.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BSgenome" version))
+ (sha256
+ (base32
+ "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
+ (properties
+ `((upstream-name . "BSgenome")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/BSgenome")
+ (synopsis "Infrastructure for Biostrings-based genome data packages")
+ (description
+ "This package provides infrastructure shared by all Biostrings-based
+genome data packages and support for efficient SNP representation.")
+ (license license:artistic2.0)))
+
(define-public r-category
(package
(name "r-category")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 32d2b6a683..9c9288c6b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,37 +7873,6 @@ including VCF header and contents in RDF and JSON.")
information about the latest version of the Gene Ontologies.")
(license license:artistic2.0)))
-(define-public r-bsgenome
- (package
- (name "r-bsgenome")
- (version "1.58.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "BSgenome" version))
- (sha256
- (base32
- "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
- (properties
- `((upstream-name . "BSgenome")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (home-page "https://bioconductor.org/packages/BSgenome")
- (synopsis "Infrastructure for Biostrings-based genome data packages")
- (description
- "This package provides infrastructure shared by all Biostrings-based
-genome data packages and support for efficient SNP representation.")
- (license license:artistic2.0)))
-
(define-public r-impute
(package
(name "r-impute")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:03 GMT) Full text and rfc822 format available.Message #23 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 07/50] gnu: r-msnbase: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:39 +0200
* gnu/packages/bioinformatics.scm (r-msnbase): Move from here...
* gnu/packages/bioconductor.scm (r-msnbase): ...to here.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 45 ---------------------------------
2 files changed, 45 insertions(+), 45 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b5787cb207..58c8336ce5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2312,6 +2312,51 @@ and the assessment of differential expression. The analysis methods apply to
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
+(define-public r-msnbase
+ (package
+ (name "r-msnbase")
+ (version "2.16.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MSnbase" version))
+ (sha256
+ (base32
+ "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h"))))
+ (properties `((upstream-name . "MSnbase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-digest" ,r-digest)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-impute" ,r-impute)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-maldiquant" ,r-maldiquant)
+ ("r-mass" ,r-mass)
+ ("r-mzid" ,r-mzid)
+ ("r-mzr" ,r-mzr)
+ ("r-pcamethods" ,r-pcamethods)
+ ("r-plyr" ,r-plyr)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-vsn" ,r-vsn)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/lgatto/MSnbase")
+ (synopsis "Base functions and classes for MS-based proteomics")
+ (description
+ "This package provides basic plotting, data manipulation and processing
+of mass spectrometry based proteomics data.")
+ (license license:artistic2.0)))
+
(define-public r-msnid
(package
(name "r-msnid")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5c2abe6e94..28893c40e7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9230,51 +9230,6 @@ the results is also provided. All PCA methods make use of the same data
structure (pcaRes) to provide a common interface to the PCA results.")
(license license:gpl3+)))
-(define-public r-msnbase
- (package
- (name "r-msnbase")
- (version "2.16.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "MSnbase" version))
- (sha256
- (base32
- "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h"))))
- (properties `((upstream-name . "MSnbase")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-digest" ,r-digest)
- ("r-ggplot2" ,r-ggplot2)
- ("r-impute" ,r-impute)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-maldiquant" ,r-maldiquant)
- ("r-mass" ,r-mass)
- ("r-mzid" ,r-mzid)
- ("r-mzr" ,r-mzr)
- ("r-pcamethods" ,r-pcamethods)
- ("r-plyr" ,r-plyr)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-vsn" ,r-vsn)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/lgatto/MSnbase")
- (synopsis "Base functions and classes for MS-based proteomics")
- (description
- "This package provides basic plotting, data manipulation and processing
-of mass spectrometry based proteomics data.")
- (license license:artistic2.0)))
-
(define-public r-aroma-light
(package
(name "r-aroma-light")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:03 GMT) Full text and rfc822 format available.Message #26 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 08/50] gnu: r-samr: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:40 +0200
* gnu/packages/cran.scm (r-samr): Move from here...
* gnu/packages/bioconductor.scm (r-samr): ...to here.
---
gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
gnu/packages/cran.scm | 30 ------------------------------
2 files changed, 31 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 58c8336ce5..f9aa34d254 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10,6 +10,7 @@
;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
+;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -2604,6 +2605,36 @@ built-in). The user may export/import tracks to/from the supported browsers,
as well as query and modify the browser state, such as the current viewport.")
(license license:artistic2.0)))
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-samr
+ (package
+ (name "r-samr")
+ (version "3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "samr" version))
+ (sha256
+ (base32
+ "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
+ (properties `((upstream-name . "samr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gsa" ,r-gsa)
+ ("r-impute" ,r-impute)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-openxlsx" ,r-openxlsx)
+ ("r-shiny" ,r-shiny)
+ ("r-shinyfiles" ,r-shinyfiles)))
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://statweb.stanford.edu/~tibs/SAM/")
+ (synopsis "Significance analysis of Microarrays")
+ (description
+ "This is a package for significance analysis of Microarrays for
+differential expression analysis, RNAseq data and related problems.")
+ ;; Any version of the LGPL
+ (license license:lgpl3+)))
+
(define-public r-shortread
(package
(name "r-shortread")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8709cd21fa..e5d1db7cb6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33,7 +33,6 @@
;;; Copyright © 2020 Magali Lemes <magalilemes00 <at> gmail.com>
;;; Copyright © 2020 Simon Tournier <zimon.toutoune <at> gmail.com>
;;; Copyright © 2020 Aniket Patil <aniket112.patil <at> gmail.com>
-;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -28629,35 +28628,6 @@ indicator, a quantitative variable or a survival time.")
;; Any version of the LGPL
(license license:lgpl3+)))
-(define-public r-samr
- (package
- (name "r-samr")
- (version "3.0")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "samr" version))
- (sha256
- (base32
- "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
- (properties `((upstream-name . "samr")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-gsa" ,r-gsa)
- ("r-impute" ,r-impute)
- ("r-matrixstats" ,r-matrixstats)
- ("r-openxlsx" ,r-openxlsx)
- ("r-shiny" ,r-shiny)
- ("r-shinyfiles" ,r-shinyfiles)))
- (native-inputs `(("gfortran" ,gfortran)))
- (home-page "https://statweb.stanford.edu/~tibs/SAM/")
- (synopsis "Significance analysis of Microarrays")
- (description
- "This is a package for significance analysis of Microarrays for
-differential expression analysis, RNAseq data and related problems.")
- ;; Any version of the LGPL
- (license license:lgpl3+)))
-
(define-public r-randomforestsrc
(package
(name "r-randomforestsrc")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:04 GMT) Full text and rfc822 format available.Message #29 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 09/50] gnu: r-impute: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:41 +0200
* gnu/packages/bioinformatics.scm (r-impute): Move from here...
* gnu/packages/bioconductor.scm (r-impute): ...to here.
---
gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
gnu/packages/bioinformatics.scm | 20 --------------------
2 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f9aa34d254..0b40d70397 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2294,6 +2294,26 @@ Enrichment Analysis} (GSEA).")
the Human Protein Atlas project.")
(license license:artistic2.0)))
+(define-public r-impute
+ (package
+ (name "r-impute")
+ (version "1.64.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "impute" version))
+ (sha256
+ (base32
+ "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/impute")
+ (synopsis "Imputation for microarray data")
+ (description
+ "This package provides a function to impute missing gene expression
+microarray data, using nearest neighbor averaging.")
+ (license license:gpl2+)))
+
(define-public r-limma
(package
(name "r-limma")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 28893c40e7..ef5c1a3323 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,26 +7873,6 @@ including VCF header and contents in RDF and JSON.")
information about the latest version of the Gene Ontologies.")
(license license:artistic2.0)))
-(define-public r-impute
- (package
- (name "r-impute")
- (version "1.64.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "impute" version))
- (sha256
- (base32
- "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
- (native-inputs
- `(("gfortran" ,gfortran)))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/impute")
- (synopsis "Imputation for microarray data")
- (description
- "This package provides a function to impute missing gene expression
-microarray data, using nearest neighbor averaging.")
- (license license:gpl2+)))
-
(define-public r-seqpattern
(package
(name "r-seqpattern")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:04 GMT) Full text and rfc822 format available.Message #32 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 10/50] gnu: r-seqpattern: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:42 +0200
* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here...
* gnu/packages/bioconductor.scm (r-seqpattern): ...to here.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 27 ---------------------------
2 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0b40d70397..1b1b00cde0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2655,6 +2655,33 @@ differential expression analysis, RNAseq data and related problems.")
;; Any version of the LGPL
(license license:lgpl3+)))
+(define-public r-seqpattern
+ (package
+ (name "r-seqpattern")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "seqPattern" version))
+ (sha256
+ (base32
+ "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))
+ (properties
+ `((upstream-name . "seqPattern")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-plotrix" ,r-plotrix)))
+ (home-page "https://bioconductor.org/packages/seqPattern")
+ (synopsis "Visualising oligonucleotide patterns and motif occurrences")
+ (description
+ "This package provides tools to visualize oligonucleotide patterns and
+sequence motif occurrences across a large set of sequences centred at a common
+reference point and sorted by a user defined feature.")
+ (license license:gpl3+)))
+
(define-public r-shortread
(package
(name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef5c1a3323..71e1481af2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,33 +7873,6 @@ including VCF header and contents in RDF and JSON.")
information about the latest version of the Gene Ontologies.")
(license license:artistic2.0)))
-(define-public r-seqpattern
- (package
- (name "r-seqpattern")
- (version "1.22.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "seqPattern" version))
- (sha256
- (base32
- "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))
- (properties
- `((upstream-name . "seqPattern")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-plotrix" ,r-plotrix)))
- (home-page "https://bioconductor.org/packages/seqPattern")
- (synopsis "Visualising oligonucleotide patterns and motif occurrences")
- (description
- "This package provides tools to visualize oligonucleotide patterns and
-sequence motif occurrences across a large set of sequences centred at a common
-reference point and sorted by a user defined feature.")
- (license license:gpl3+)))
-
(define-public r-genomation
(package
(name "r-genomation")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:04 GMT) Full text and rfc822 format available.Message #35 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 11/50] gnu: r-go-db: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:43 +0200
* gnu/packages/bioinformatics.scm (r-go-db): Move from here...
* gnu/packages/bioconductor.scm (r-go-db): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.
---
gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 24 ------------------------
2 files changed, 22 insertions(+), 24 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1b1b00cde0..eb73909723 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -413,6 +413,28 @@ in Biostrings objects.")
ID and species. It is used by functions in the GenomeInfoDb package.")
(license license:artistic2.0)))
+(define-public r-go-db
+ (package
+ (name "r-go-db")
+ (version "3.7.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GO.db" version 'annotation))
+ (sha256
+ (base32
+ "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
+ (properties
+ `((upstream-name . "GO.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://bioconductor.org/packages/GO.db")
+ (synopsis "Annotation maps describing the entire Gene Ontology")
+ (description
+ "The purpose of this GO.db annotation package is to provide detailed
+information about the latest version of the Gene Ontologies.")
+ (license license:artistic2.0)))
+
(define-public r-homo-sapiens
(package
(name "r-homo-sapiens")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71e1481af2..71f07748b6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,30 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-go-db
- (package
- (name "r-go-db")
- (version "3.7.0")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/GO.db_"
- version ".tar.gz"))
- (sha256
- (base32
- "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
- (properties
- `((upstream-name . "GO.db")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
- (home-page "https://bioconductor.org/packages/GO.db")
- (synopsis "Annotation maps describing the entire Gene Ontology")
- (description
- "The purpose of this GO.db annotation package is to provide detailed
-information about the latest version of the Gene Ontologies.")
- (license license:artistic2.0)))
-
(define-public r-genomation
(package
(name "r-genomation")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:05 GMT) Full text and rfc822 format available.Message #38 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 12/50] gnu: r-genomation: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:44 +0200
* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
---
gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 48 ---------------------------------
2 files changed, 48 insertions(+), 48 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eb73909723..2be7920770 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2099,6 +2099,54 @@ CAGE.")
high-throughput sequencing experiments.")
(license license:artistic2.0)))
+(define-public r-genomation
+ (package
+ (name "r-genomation")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genomation" version))
+ (sha256
+ (base32
+ "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-data-table" ,r-data-table)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridbase" ,r-gridbase)
+ ("r-impute" ,r-impute)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-plotrix" ,r-plotrix)
+ ("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-readr" ,r-readr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-runit" ,r-runit)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqpattern" ,r-seqpattern)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+ (synopsis "Summary, annotation and visualization of genomic data")
+ (description
+ "This package provides a package for summary and annotation of genomic
+intervals. Users can visualize and quantify genomic intervals over
+pre-defined functional regions, such as promoters, exons, introns, etc. The
+genomic intervals represent regions with a defined chromosome position, which
+may be associated with a score, such as aligned reads from HT-seq experiments,
+TF binding sites, methylation scores, etc. The package can use any tabular
+genomic feature data as long as it has minimal information on the locations of
+genomic intervals. In addition, it can use BAM or BigWig files as input.")
+ (license license:artistic2.0)))
+
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71f07748b6..f8e7b2cab9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-genomation
- (package
- (name "r-genomation")
- (version "1.22.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "genomation" version))
- (sha256
- (base32
- "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-data-table" ,r-data-table)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridbase" ,r-gridbase)
- ("r-impute" ,r-impute)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-plotrix" ,r-plotrix)
- ("r-plyr" ,r-plyr)
- ("r-rcpp" ,r-rcpp)
- ("r-readr" ,r-readr)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-runit" ,r-runit)
- ("r-s4vectors" ,r-s4vectors)
- ("r-seqpattern" ,r-seqpattern)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
- (synopsis "Summary, annotation and visualization of genomic data")
- (description
- "This package provides a package for summary and annotation of genomic
-intervals. Users can visualize and quantify genomic intervals over
-pre-defined functional regions, such as promoters, exons, introns, etc. The
-genomic intervals represent regions with a defined chromosome position, which
-may be associated with a score, such as aligned reads from HT-seq experiments,
-TF binding sites, methylation scores, etc. The package can use any tabular
-genomic feature data as long as it has minimal information on the locations of
-genomic intervals. In addition, it can use BAM or BigWig files as input.")
- (license license:artistic2.0)))
-
(define-public r-genomationdata
(package
(name "r-genomationdata")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:05 GMT) Full text and rfc822 format available.Message #41 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 04/50] gnu: r-topgo: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:36 +0200
* gnu/packages/bioinformatics.scm (r-topgo): Move from here...
* gnu/packages/bioconductor.scm (r-topgo): ...to here.
---
gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 33 ---------------------------------
2 files changed, 33 insertions(+), 33 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2263c17cc4..2afb5214ee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2607,6 +2607,39 @@ experimental designs is facilitated by a consistently implemented sample
annotation infrastructure.")
(license license:artistic2.0)))
+(define-public r-topgo
+ (package
+ (name "r-topgo")
+ (version "2.42.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "topGO" version))
+ (sha256
+ (base32
+ "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
+ (properties
+ `((upstream-name . "topGO")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-dbi" ,r-dbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-lattice" ,r-lattice)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-sparsem" ,r-sparsem)))
+ (home-page "https://bioconductor.org/packages/topGO")
+ (synopsis "Enrichment analysis for gene ontology")
+ (description
+ "The topGO package provides tools for testing @dfn{gene ontology} (GO)
+terms while accounting for the topology of the GO graph. Different test
+statistics and different methods for eliminating local similarities and
+dependencies between GO terms can be implemented and applied.")
+ ;; Any version of the LGPL applies.
+ (license license:lgpl2.1+)))
+
(define-public r-variantannotation
(package
(name "r-variantannotation")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bf8cb2f3a5..32d2b6a683 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,39 +7873,6 @@ including VCF header and contents in RDF and JSON.")
information about the latest version of the Gene Ontologies.")
(license license:artistic2.0)))
-(define-public r-topgo
- (package
- (name "r-topgo")
- (version "2.42.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "topGO" version))
- (sha256
- (base32
- "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
- (properties
- `((upstream-name . "topGO")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-dbi" ,r-dbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-go-db" ,r-go-db)
- ("r-graph" ,r-graph)
- ("r-lattice" ,r-lattice)
- ("r-matrixstats" ,r-matrixstats)
- ("r-sparsem" ,r-sparsem)))
- (home-page "https://bioconductor.org/packages/topGO")
- (synopsis "Enrichment analysis for gene ontology")
- (description
- "The topGO package provides tools for testing @dfn{gene ontology} (GO)
-terms while accounting for the topology of the GO graph. Different test
-statistics and different methods for eliminating local similarities and
-dependencies between GO terms can be implemented and applied.")
- ;; Any version of the LGPL applies.
- (license license:lgpl2.1+)))
-
(define-public r-bsgenome
(package
(name "r-bsgenome")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:06 GMT) Full text and rfc822 format available.Message #44 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 13/50] gnu: r-genomationdata: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:45 +0200
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 28 ----------------------------
2 files changed, 26 insertions(+), 28 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2be7920770..22b5a6068e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1021,6 +1021,32 @@ chromstaR package.")
genomes and gene ID formats, largely based on the UCSC table browser.")
(license license:lgpl2.0+)))
+(define-public r-genomationdata
+ (package
+ (name "r-genomationdata")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genomationData" version 'experiment))
+ (sha256
+ (base32
+ "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
+ (properties
+ `((upstream-name . "genomationData")))
+ (build-system r-build-system)
+ ;; As this package provides little more than large data files, it doesn't
+ ;; make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+ (synopsis "Experimental data for use with the genomation package")
+ (description
+ "This package contains experimental genetic data for use with the
+genomation package. Included are Chip Seq, Methylation and Cage data,
+downloaded from Encode.")
+ (license license:gpl3+)))
+
(define-public r-pasilla
(package
(name "r-pasilla")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f8e7b2cab9..87254a9058 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,34 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-genomationdata
- (package
- (name "r-genomationdata")
- (version "1.22.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "genomationData_" version ".tar.gz"))
- (sha256
- (base32
- "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
- (build-system r-build-system)
- ;; As this package provides little more than large data files, it doesn't
- ;; make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
- (synopsis "Experimental data for use with the genomation package")
- (description
- "This package contains experimental genetic data for use with the
-genomation package. Included are Chip Seq, Methylation and Cage data,
-downloaded from Encode.")
- (license license:gpl3+)))
-
(define-public r-seqlogo
(package
(name "r-seqlogo")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:06 GMT) Full text and rfc822 format available.Message #47 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 14/50] gnu: r-pcamethods: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:46 +0200
* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here...
* gnu/packages/bioconductor.scm (r-pcamethods): ...to here.
---
gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 30 ------------------------------
2 files changed, 30 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 22b5a6068e..1533e5b8f9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2526,6 +2526,36 @@ contains a number of utilities to explore the MS/MS results and assess missed
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
+(define-public r-pcamethods
+ (package
+ (name "r-pcamethods")
+ (version "1.82.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "pcaMethods" version))
+ (sha256
+ (base32
+ "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0"))))
+ (properties `((upstream-name . "pcaMethods")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-mass" ,r-mass)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/hredestig/pcamethods")
+ (synopsis "Collection of PCA methods")
+ (description
+ "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
+Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
+for missing value estimation is included for comparison. BPCA, PPCA and
+NipalsPCA may be used to perform PCA on incomplete data as well as for
+accurate missing value estimation. A set of methods for printing and plotting
+the results is also provided. All PCA methods make use of the same data
+structure (pcaRes) to provide a common interface to the PCA results.")
+ (license license:gpl3+)))
+
(define-public r-rbgl
(package
(name "r-rbgl")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87254a9058..a98f3d5d8a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9053,36 +9053,6 @@ mzIdentML files with the drawback of having less pretty output than a vendor
specific parser.")
(license license:gpl2+)))
-(define-public r-pcamethods
- (package
- (name "r-pcamethods")
- (version "1.82.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "pcaMethods" version))
- (sha256
- (base32
- "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0"))))
- (properties `((upstream-name . "pcaMethods")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-mass" ,r-mass)
- ("r-rcpp" ,r-rcpp)))
- (home-page "https://github.com/hredestig/pcamethods")
- (synopsis "Collection of PCA methods")
- (description
- "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
-Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
-for missing value estimation is included for comparison. BPCA, PPCA and
-NipalsPCA may be used to perform PCA on incomplete data as well as for
-accurate missing value estimation. A set of methods for printing and plotting
-the results is also provided. All PCA methods make use of the same data
-structure (pcaRes) to provide a common interface to the PCA results.")
- (license license:gpl3+)))
-
(define-public r-aroma-light
(package
(name "r-aroma-light")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:06 GMT) Full text and rfc822 format available.Message #50 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 15/50] gnu: r-mzid: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:47 +0200
* gnu/packages/bioinformatics.scm (r-mzid): Move from here...
* gnu/packages/bioconductor.scm (r-mzid): ...to here.
---
gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1533e5b8f9..5e0b722e2f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2526,6 +2526,37 @@ contains a number of utilities to explore the MS/MS results and assess missed
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
+(define-public r-mzid
+ (package
+ (name "r-mzid")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "mzID" version))
+ (sha256
+ (base32
+ "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2"))))
+ (properties `((upstream-name . "mzID")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-iterators" ,r-iterators)
+ ("r-plyr" ,r-plyr)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/mzID")
+ (synopsis "Parser for mzIdentML files")
+ (description
+ "This package provides a parser for mzIdentML files implemented using the
+XML package. The parser tries to be general and able to handle all types of
+mzIdentML files with the drawback of having less pretty output than a vendor
+specific parser.")
+ (license license:gpl2+)))
+
(define-public r-pcamethods
(package
(name "r-pcamethods")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a98f3d5d8a..5b6426e17d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-mzid
- (package
- (name "r-mzid")
- (version "1.28.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "mzID" version))
- (sha256
- (base32
- "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2"))))
- (properties `((upstream-name . "mzID")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-iterators" ,r-iterators)
- ("r-plyr" ,r-plyr)
- ("r-protgenerics" ,r-protgenerics)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/mzID")
- (synopsis "Parser for mzIdentML files")
- (description
- "This package provides a parser for mzIdentML files implemented using the
-XML package. The parser tries to be general and able to handle all types of
-mzIdentML files with the drawback of having less pretty output than a vendor
-specific parser.")
- (license license:gpl2+)))
-
(define-public r-aroma-light
(package
(name "r-aroma-light")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:07 GMT) Full text and rfc822 format available.Message #53 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 16/50] gnu: r-aroma-light: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:48 +0200
* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here...
* gnu/packages/bioconductor.scm (r-aroma-light): ...to here.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 27 ---------------------------
2 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5e0b722e2f..e58cd66fef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1782,6 +1782,33 @@ annotation data packages using SQLite data storage.")
databases. Packages produced are intended to be used with AnnotationDbi.")
(license license:artistic2.0)))
+(define-public r-aroma-light
+ (package
+ (name "r-aroma-light")
+ (version "3.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "aroma.light" version))
+ (sha256
+ (base32
+ "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0"))))
+ (properties `((upstream-name . "aroma.light")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrixstats" ,r-matrixstats)
+ ("r-r-methodss3" ,r-r-methodss3)
+ ("r-r-oo" ,r-r-oo)
+ ("r-r-utils" ,r-r-utils)))
+ (home-page "https://github.com/HenrikBengtsson/aroma.light")
+ (synopsis "Methods for normalization and visualization of microarray data")
+ (description
+ "This package provides methods for microarray analysis that take basic
+data types such as matrices and lists of vectors. These methods can be used
+standalone, be utilized in other packages, or be wrapped up in higher-level
+classes.")
+ (license license:gpl2+)))
+
(define-public r-biobase
(package
(name "r-biobase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5b6426e17d..c8444eea9f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,33 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-aroma-light
- (package
- (name "r-aroma-light")
- (version "3.20.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "aroma.light" version))
- (sha256
- (base32
- "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0"))))
- (properties `((upstream-name . "aroma.light")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-matrixstats" ,r-matrixstats)
- ("r-r-methodss3" ,r-r-methodss3)
- ("r-r-oo" ,r-r-oo)
- ("r-r-utils" ,r-r-utils)))
- (home-page "https://github.com/HenrikBengtsson/aroma.light")
- (synopsis "Methods for normalization and visualization of microarray data")
- (description
- "This package provides methods for microarray analysis that take basic
-data types such as matrices and lists of vectors. These methods can be used
-standalone, be utilized in other packages, or be wrapped up in higher-level
-classes.")
- (license license:gpl2+)))
-
(define-public r-deseq
(package
(name "r-deseq")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:07 GMT) Full text and rfc822 format available.Message #56 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 18/50] gnu: r-edaseq: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:50 +0200
* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...
* gnu/packages/bioconductor.scm (r-edaseq): ...to here.
---
gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 40 ---------------------------------
2 files changed, 40 insertions(+), 40 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 69ef513bc6..beb662984d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2127,6 +2127,46 @@ testing. The package also provides functions for the visualization and
exploration of the results.")
(license license:gpl3+)))
+(define-public r-edaseq
+ (package
+ (name "r-edaseq")
+ (version "2.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EDASeq" version))
+ (sha256
+ (base32
+ "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
+ (properties `((upstream-name . "EDASeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-aroma-light" ,r-aroma-light)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-shortread" ,r-shortread)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/drisso/EDASeq")
+ (synopsis "Exploratory data analysis and normalization for RNA-Seq")
+ (description
+ "This package provides support for numerical and graphical summaries of
+RNA-Seq genomic read data. Provided within-lane normalization procedures to
+adjust for GC-content effect (or other gene-level effects) on read counts:
+loess robust local regression, global-scaling, and full-quantile
+normalization. Between-lane normalization procedures to adjust for
+distributional differences between lanes (e.g., sequencing depth):
+global-scaling and full-quantile normalization.")
+ (license license:artistic2.0)))
+
(define-public r-edger
(package
(name "r-edger")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2edb501f9b..b0de0d9880 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,46 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-edaseq
- (package
- (name "r-edaseq")
- (version "2.24.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "EDASeq" version))
- (sha256
- (base32
- "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
- (properties `((upstream-name . "EDASeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-aroma-light" ,r-aroma-light)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-shortread" ,r-shortread)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/drisso/EDASeq")
- (synopsis "Exploratory data analysis and normalization for RNA-Seq")
- (description
- "This package provides support for numerical and graphical summaries of
-RNA-Seq genomic read data. Provided within-lane normalization procedures to
-adjust for GC-content effect (or other gene-level effects) on read counts:
-loess robust local regression, global-scaling, and full-quantile
-normalization. Between-lane normalization procedures to adjust for
-distributional differences between lanes (e.g., sequencing depth):
-global-scaling and full-quantile normalization.")
- (license license:artistic2.0)))
-
(define-public r-interactivedisplaybase
(package
(name "r-interactivedisplaybase")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:08 GMT) Full text and rfc822 format available.Message #59 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 17/50] gnu: r-deseq: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:49 +0200
* gnu/packages/bioinformatics.scm (r-deseq): Move from here...
* gnu/packages/bioconductor.scm (r-deseq): ...to here.
---
gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e58cd66fef..69ef513bc6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2013,6 +2013,37 @@ genome data packages and support for efficient SNP representation.")
analysis.")
(license license:artistic2.0)))
+(define-public r-deseq
+ (package
+ (name "r-deseq")
+ (version "1.39.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DESeq" version))
+ (sha256
+ (base32
+ "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
+ (properties `((upstream-name . "DESeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-lattice" ,r-lattice)
+ ("r-locfit" ,r-locfit)
+ ("r-mass" ,r-mass)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "https://www-huber.embl.de/users/anders/DESeq/")
+ (synopsis "Differential gene expression analysis")
+ (description
+ "This package provides tools for estimating variance-mean dependence in
+count data from high-throughput genetic sequencing assays and for testing for
+differential expression based on a model using the negative binomial
+distribution.")
+ (license license:gpl3+)))
+
(define-public r-deseq2
(package
(name "r-deseq2")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c8444eea9f..2edb501f9b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-deseq
- (package
- (name "r-deseq")
- (version "1.39.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DESeq" version))
- (sha256
- (base32
- "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
- (properties `((upstream-name . "DESeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genefilter" ,r-genefilter)
- ("r-geneplotter" ,r-geneplotter)
- ("r-lattice" ,r-lattice)
- ("r-locfit" ,r-locfit)
- ("r-mass" ,r-mass)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
- (home-page "https://www-huber.embl.de/users/anders/DESeq/")
- (synopsis "Differential gene expression analysis")
- (description
- "This package provides tools for estimating variance-mean dependence in
-count data from high-throughput genetic sequencing assays and for testing for
-differential expression based on a model using the negative binomial
-distribution.")
- (license license:gpl3+)))
-
(define-public r-edaseq
(package
(name "r-edaseq")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:08 GMT) Full text and rfc822 format available.Message #62 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 19/50] gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:51 +0200
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...
* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 27 ---------------------------
2 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index beb662984d..9619ce5464 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2508,6 +2508,33 @@ the Human Protein Atlas project.")
microarray data, using nearest neighbor averaging.")
(license license:gpl2+)))
+(define-public r-interactivedisplaybase
+ (package
+ (name "r-interactivedisplaybase")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "interactiveDisplayBase" version))
+ (sha256
+ (base32
+ "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01"))))
+ (properties
+ `((upstream-name . "interactiveDisplayBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-dt" ,r-dt)
+ ("r-shiny" ,r-shiny)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
+ (synopsis "Base package for web displays of Bioconductor objects")
+ (description
+ "This package contains the basic methods needed to generate interactive
+Shiny-based display methods for Bioconductor objects.")
+ (license license:artistic2.0)))
+
(define-public r-limma
(package
(name "r-limma")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b0de0d9880..b367dcae98 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,33 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-interactivedisplaybase
- (package
- (name "r-interactivedisplaybase")
- (version "1.28.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "interactiveDisplayBase" version))
- (sha256
- (base32
- "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01"))))
- (properties
- `((upstream-name . "interactiveDisplayBase")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-dt" ,r-dt)
- ("r-shiny" ,r-shiny)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
- (synopsis "Base package for web displays of Bioconductor objects")
- (description
- "This package contains the basic methods needed to generate interactive
-Shiny-based display methods for Bioconductor objects.")
- (license license:artistic2.0)))
-
(define-public r-annotationhub
(package
(name "r-annotationhub")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:08 GMT) Full text and rfc822 format available.Message #65 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 20/50] gnu: r-annotationhub: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:52 +0200
* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...
* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
---
gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 41 ---------------------------------
2 files changed, 41 insertions(+), 41 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9619ce5464..4657b0fa8b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1782,6 +1782,47 @@ annotation data packages using SQLite data storage.")
databases. Packages produced are intended to be used with AnnotationDbi.")
(license license:artistic2.0)))
+(define-public r-annotationhub
+ (package
+ (name "r-annotationhub")
+ (version "2.22.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationHub" version))
+ (sha256
+ (base32
+ "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5"))))
+ (properties `((upstream-name . "AnnotationHub")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocfilecache" ,r-biocfilecache)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biocversion" ,r-biocversion)
+ ("r-curl" ,r-curl)
+ ("r-dplyr" ,r-dplyr)
+ ("r-httr" ,r-httr)
+ ("r-interactivedisplaybase" ,r-interactivedisplaybase)
+ ("r-rappdirs" ,r-rappdirs)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/AnnotationHub")
+ (synopsis "Client to access AnnotationHub resources")
+ (description
+ "This package provides a client for the Bioconductor AnnotationHub web
+resource. The AnnotationHub web resource provides a central location where
+genomic files (e.g. VCF, bed, wig) and other resources from standard
+locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
+metadata about each resource, e.g., a textual description, tags, and date of
+modification. The client creates and manages a local cache of files retrieved
+by the user, helping with quick and reproducible access.")
+ (license license:artistic2.0)))
+
(define-public r-aroma-light
(package
(name "r-aroma-light")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b367dcae98..1dc2d6f977 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,47 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-annotationhub
- (package
- (name "r-annotationhub")
- (version "2.22.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "AnnotationHub" version))
- (sha256
- (base32
- "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5"))))
- (properties `((upstream-name . "AnnotationHub")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biocversion" ,r-biocversion)
- ("r-curl" ,r-curl)
- ("r-dplyr" ,r-dplyr)
- ("r-httr" ,r-httr)
- ("r-interactivedisplaybase" ,r-interactivedisplaybase)
- ("r-rappdirs" ,r-rappdirs)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)
- ("r-yaml" ,r-yaml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/AnnotationHub")
- (synopsis "Client to access AnnotationHub resources")
- (description
- "This package provides a client for the Bioconductor AnnotationHub web
-resource. The AnnotationHub web resource provides a central location where
-genomic files (e.g. VCF, bed, wig) and other resources from standard
-locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
-metadata about each resource, e.g., a textual description, tags, and date of
-modification. The client creates and manages a local cache of files retrieved
-by the user, helping with quick and reproducible access.")
- (license license:artistic2.0)))
-
(define-public r-fastseg
(package
(name "r-fastseg")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:09 GMT) Full text and rfc822 format available.Message #68 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 21/50] gnu: r-fastseg: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:53 +0200
* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...
* gnu/packages/bioconductor.scm (r-fastseg): ...to here.
---
gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 30 ------------------------------
2 files changed, 30 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4657b0fa8b..313ed7e36f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2236,6 +2236,36 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and
CAGE.")
(license license:gpl2+)))
+(define-public r-fastseg
+ (package
+ (name "r-fastseg")
+ (version "1.36.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "fastseg" version))
+ (sha256
+ (base32
+ "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
+ (synopsis "Fast segmentation algorithm for genetic sequencing data")
+ (description
+ "Fastseg implements a very fast and efficient segmentation algorithm.
+It can segment data from DNA microarrays and data from next generation
+sequencing for example to detect copy number segments. Further it can segment
+data from RNA microarrays like tiling arrays to identify transcripts. Most
+generally, it can segment data given as a matrix or as a vector. Various data
+formats can be used as input to fastseg like expression set objects for
+microarrays or GRanges for sequencing data.")
+ (license license:lgpl2.0+)))
+
(define-public r-genefilter
(package
(name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1dc2d6f977..33680c283d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,36 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-fastseg
- (package
- (name "r-fastseg")
- (version "1.36.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "fastseg" version))
- (sha256
- (base32
- "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
- (synopsis "Fast segmentation algorithm for genetic sequencing data")
- (description
- "Fastseg implements a very fast and efficient segmentation algorithm.
-It can segment data from DNA microarrays and data from next generation
-sequencing for example to detect copy number segments. Further it can segment
-data from RNA microarrays like tiling arrays to identify transcripts. Most
-generally, it can segment data given as a matrix or as a vector. Various data
-formats can be used as input to fastseg like expression set objects for
-microarrays or GRanges for sequencing data.")
- (license license:lgpl2.0+)))
-
(define-public r-keggrest
(package
(name "r-keggrest")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:09 GMT) Full text and rfc822 format available.Message #71 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 22/50] gnu: r-affy: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:54 +0200
* gnu/packages/bioinformatics.scm (r-affy): Move from here...
* gnu/packages/bioconductor.scm (r-affy): ...to here.
---
gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 28 ----------------------------
2 files changed, 28 insertions(+), 28 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 313ed7e36f..6d60b5884c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1550,6 +1550,34 @@ optimized in C++, and the main interface function provides an easy way of
performing parallel computations on multicore machines.")
(license license:gpl2+)))
+(define-public r-affy
+ (package
+ (name "r-affy")
+ (version "1.68.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affy" version))
+ (sha256
+ (base32
+ "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affyio" ,r-affyio)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://bioconductor.org/packages/affy")
+ (synopsis "Methods for affymetrix oligonucleotide arrays")
+ (description
+ "This package contains functions for exploratory oligonucleotide array
+analysis.")
+ (license license:lgpl2.0+)))
+
(define-public r-affycomp
(package
(name "r-affycomp")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 33680c283d..b789ecd977 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8958,34 +8958,6 @@ upon file format information. The primary focus is on accessing the CEL and
CDF file formats.")
(license license:lgpl2.0+)))
-(define-public r-affy
- (package
- (name "r-affy")
- (version "1.68.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "affy" version))
- (sha256
- (base32
- "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-affyio" ,r-affyio)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-zlibbioc" ,r-zlibbioc)))
- (inputs
- `(("zlib" ,zlib)))
- (home-page "https://bioconductor.org/packages/affy")
- (synopsis "Methods for affymetrix oligonucleotide arrays")
- (description
- "This package contains functions for exploratory oligonucleotide array
-analysis.")
- (license license:lgpl2.0+)))
-
(define-public r-vsn
(package
(name "r-vsn")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:10 GMT) Full text and rfc822 format available.Message #74 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 23/50] gnu: r-keggrest: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:55 +0200
* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...
* gnu/packages/bioconductor.scm (r-keggrest): ...to here.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 26 --------------------------
2 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6d60b5884c..5ee670e858 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2634,6 +2634,32 @@ microarray data, using nearest neighbor averaging.")
Shiny-based display methods for Bioconductor objects.")
(license license:artistic2.0)))
+(define-public r-keggrest
+ (package
+ (name "r-keggrest")
+ (version "1.30.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "KEGGREST" version))
+ (sha256
+ (base32
+ "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))
+ (properties `((upstream-name . "KEGGREST")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-httr" ,r-httr)
+ ("r-png" ,r-png)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/KEGGREST")
+ (synopsis "Client-side REST access to KEGG")
+ (description
+ "This package provides a package that provides a client interface to the
+@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
+ (license license:artistic2.0)))
+
(define-public r-limma
(package
(name "r-limma")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b789ecd977..5dacf8a342 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,32 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-keggrest
- (package
- (name "r-keggrest")
- (version "1.30.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "KEGGREST" version))
- (sha256
- (base32
- "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))
- (properties `((upstream-name . "KEGGREST")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-httr" ,r-httr)
- ("r-png" ,r-png)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/KEGGREST")
- (synopsis "Client-side REST access to KEGG")
- (description
- "This package provides a package that provides a client interface to the
-@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
- (license license:artistic2.0)))
-
(define-public r-gage
(package
(name "r-gage")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:10 GMT) Full text and rfc822 format available.Message #77 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 24/50] gnu: r-gage: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:56 +0200
* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
---
gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++-
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5ee670e858..f6d3ef897a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
;;; Copyright © 2016 Pjotr Prins <pjotr.guix <at> thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben <at> gmail.com>
;;; Copyright © 2017 Efraim Flashner <efraim <at> flashner.co.il>
-;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me <at> tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me <at> tobias.gr>
;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau <at> gmail.com>
;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
@@ -2294,6 +2294,37 @@ formats can be used as input to fastseg like expression set objects for
microarrays or GRanges for sequencing data.")
(license license:lgpl2.0+)))
+(define-public r-gage
+ (package
+ (name "r-gage")
+ (version "2.40.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gage" version))
+ (sha256
+ (base32
+ "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-keggrest" ,r-keggrest)))
+ (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
+ "articles/10.1186/1471-2105-10-161"))
+ (synopsis "Generally applicable gene-set enrichment for pathway analysis")
+ (description
+ "GAGE is a published method for gene set (enrichment or GSEA) or pathway
+analysis. GAGE is generally applicable independent of microarray or RNA-Seq
+data attributes including sample sizes, experimental designs, assay platforms,
+and other types of heterogeneity. The gage package provides functions for
+basic GAGE analysis, result processing and presentation. In addition, it
+provides demo microarray data and commonly used gene set data based on KEGG
+pathways and GO terms. These functions and data are also useful for gene set
+analysis using other methods.")
+ (license license:gpl2+)))
+
(define-public r-genefilter
(package
(name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5dacf8a342..daf1fb6958 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,37 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-gage
- (package
- (name "r-gage")
- (version "2.40.2")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "gage" version))
- (sha256
- (base32
- "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-go-db" ,r-go-db)
- ("r-graph" ,r-graph)
- ("r-keggrest" ,r-keggrest)))
- (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
- "articles/10.1186/1471-2105-10-161"))
- (synopsis "Generally applicable gene-set enrichment for pathway analysis")
- (description
- "GAGE is a published method for gene set (enrichment or GSEA) or pathway
-analysis. GAGE is generally applicable independent of microarray or RNA-Seq
-data attributes including sample sizes, experimental designs, assay platforms,
-and other types of heterogeneity. The gage package provides functions for
-basic GAGE analysis, result processing and presentation. In addition, it
-provides demo microarray data and commonly used gene set data based on KEGG
-pathways and GO terms. These functions and data are also useful for gene set
-analysis using other methods.")
- (license license:gpl2+)))
-
(define-public r-genomicfiles
(package
(name "r-genomicfiles")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:10 GMT) Full text and rfc822 format available.Message #80 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 25/50] gnu: r-complexheatmap: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:57 +0200
* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...
* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
---
gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 39 ---------------------------------
2 files changed, 39 insertions(+), 39 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f6d3ef897a..92eb5a0906 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2082,6 +2082,45 @@ genome data packages and support for efficient SNP representation.")
analysis.")
(license license:artistic2.0)))
+(define-public r-complexheatmap
+ (package
+ (name "r-complexheatmap")
+ (version "2.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ComplexHeatmap" version))
+ (sha256
+ (base32
+ "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))
+ (properties
+ `((upstream-name . "ComplexHeatmap")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cairo" ,r-cairo)
+ ("r-circlize" ,r-circlize)
+ ("r-clue" ,r-clue)
+ ("r-colorspace" ,r-colorspace)
+ ("r-digest" ,r-digest)
+ ("r-getoptlong" ,r-getoptlong)
+ ("r-globaloptions" ,r-globaloptions)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-png" ,r-png)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://github.com/jokergoo/ComplexHeatmap")
+ (synopsis "Making Complex Heatmaps")
+ (description
+ "Complex heatmaps are efficient to visualize associations between
+different sources of data sets and reveal potential structures. This package
+provides a highly flexible way to arrange multiple heatmaps and supports
+self-defined annotation graphics.")
+ (license license:gpl2+)))
+
(define-public r-deseq
(package
(name "r-deseq")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index daf1fb6958..acaf41acc4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9028,45 +9028,6 @@ distributed by file or by range. User defined mapper and reducer functions
provide added flexibility for data combination and manipulation.")
(license license:artistic2.0)))
-(define-public r-complexheatmap
- (package
- (name "r-complexheatmap")
- (version "2.6.2")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ComplexHeatmap" version))
- (sha256
- (base32
- "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))
- (properties
- `((upstream-name . "ComplexHeatmap")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-cairo" ,r-cairo)
- ("r-circlize" ,r-circlize)
- ("r-clue" ,r-clue)
- ("r-colorspace" ,r-colorspace)
- ("r-digest" ,r-digest)
- ("r-getoptlong" ,r-getoptlong)
- ("r-globaloptions" ,r-globaloptions)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-png" ,r-png)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page
- "https://github.com/jokergoo/ComplexHeatmap")
- (synopsis "Making Complex Heatmaps")
- (description
- "Complex heatmaps are efficient to visualize associations between
-different sources of data sets and reveal potential structures. This package
-provides a highly flexible way to arrange multiple heatmaps and supports
-self-defined annotation graphics.")
- (license license:gpl2+)))
-
(define-public r-dirichletmultinomial
(package
(name "r-dirichletmultinomial")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:11 GMT) Full text and rfc822 format available.Message #83 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 26/50] gnu: r-genomicfiles: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:58 +0200
* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
---
gnu/packages/bioconductor.scm | 34 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 34 ---------------------------------
2 files changed, 34 insertions(+), 34 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 92eb5a0906..e73e78f616 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2546,6 +2546,40 @@ transcripts, exons, cds and genes. Flexible methods are provided for
extracting the desired features in a convenient format.")
(license license:artistic2.0)))
+(define-public r-genomicfiles
+ (package
+ (name "r-genomicfiles")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicFiles" version))
+ (sha256
+ (base32
+ "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz"))))
+ (properties `((upstream-name . "GenomicFiles")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixgenerics" ,r-matrixgenerics)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/GenomicFiles")
+ (synopsis "Distributed computing by file or by range")
+ (description
+ "This package provides infrastructure for parallel computations
+distributed by file or by range. User defined mapper and reducer functions
+provide added flexibility for data combination and manipulation.")
+ (license license:artistic2.0)))
+
(define-public r-genomicranges
(package
(name "r-genomicranges")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index acaf41acc4..4836eee82c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,40 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-genomicfiles
- (package
- (name "r-genomicfiles")
- (version "1.26.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomicFiles" version))
- (sha256
- (base32
- "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz"))))
- (properties `((upstream-name . "GenomicFiles")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrixgenerics" ,r-matrixgenerics)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (home-page "https://bioconductor.org/packages/GenomicFiles")
- (synopsis "Distributed computing by file or by range")
- (description
- "This package provides infrastructure for parallel computations
-distributed by file or by range. User defined mapper and reducer functions
-provide added flexibility for data combination and manipulation.")
- (license license:artistic2.0)))
-
(define-public r-dirichletmultinomial
(package
(name "r-dirichletmultinomial")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:11 GMT) Full text and rfc822 format available.Message #86 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 27/50] gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:25:59 +0200
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
---
gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 29 -----------------------------
2 files changed, 29 insertions(+), 29 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e73e78f616..7717c821b9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2235,6 +2235,35 @@ testing. The package also provides functions for the visualization and
exploration of the results.")
(license license:gpl3+)))
+(define-public r-dirichletmultinomial
+ (package
+ (name "r-dirichletmultinomial")
+ (version "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DirichletMultinomial" version))
+ (sha256
+ (base32
+ "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))
+ (properties
+ `((upstream-name . "DirichletMultinomial")))
+ (build-system r-build-system)
+ (inputs
+ `(("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/DirichletMultinomial")
+ (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
+ (description
+ "Dirichlet-multinomial mixture models can be used to describe variability
+in microbial metagenomic data. This package is an interface to code
+originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
+1-15.")
+ (license license:lgpl3)))
+
(define-public r-edaseq
(package
(name "r-edaseq")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4836eee82c..0c7b3d602f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,35 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.")
(license license:artistic2.0)))
-(define-public r-dirichletmultinomial
- (package
- (name "r-dirichletmultinomial")
- (version "1.32.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DirichletMultinomial" version))
- (sha256
- (base32
- "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))
- (properties
- `((upstream-name . "DirichletMultinomial")))
- (build-system r-build-system)
- (inputs
- `(("gsl" ,gsl)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://bioconductor.org/packages/DirichletMultinomial")
- (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
- (description
- "Dirichlet-multinomial mixture models can be used to describe variability
-in microbial metagenomic data. This package is an interface to code
-originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
-1-15.")
- (license license:lgpl3)))
-
(define-public r-ensembldb
(package
(name "r-ensembldb")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:11 GMT) Full text and rfc822 format available.Message #89 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 28/50] gnu: r-organismdbi: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:00 +0200
* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...
* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
---
gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 32 --------------------------------
2 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7717c821b9..c63d39dc9c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2940,6 +2940,38 @@ mzIdentML files with the drawback of having less pretty output than a vendor
specific parser.")
(license license:gpl2+)))
+(define-public r-organismdbi
+ (package
+ (name "r-organismdbi")
+ (version "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "OrganismDbi" version))
+ (sha256
+ (base32
+ "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))
+ (properties `((upstream-name . "OrganismDbi")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-dbi" ,r-dbi)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-graph" ,r-graph)
+ ("r-iranges" ,r-iranges)
+ ("r-rbgl" ,r-rbgl)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/OrganismDbi")
+ (synopsis "Software to enable the smooth interfacing of database packages")
+ (description "The package enables a simple unified interface to several
+annotation packages each of which has its own schema by taking advantage of
+the fact that each of these packages implements a select methods.")
+ (license license:artistic2.0)))
+
(define-public r-pcamethods
(package
(name "r-pcamethods")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0c7b3d602f..1c90700c95 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9039,38 +9039,6 @@ chromosome region or transcript models of lincRNA genes.")
;; No version specified
(license license:lgpl3+)))
-(define-public r-organismdbi
- (package
- (name "r-organismdbi")
- (version "1.32.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "OrganismDbi" version))
- (sha256
- (base32
- "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))
- (properties `((upstream-name . "OrganismDbi")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-dbi" ,r-dbi)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-graph" ,r-graph)
- ("r-iranges" ,r-iranges)
- ("r-rbgl" ,r-rbgl)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://bioconductor.org/packages/OrganismDbi")
- (synopsis "Software to enable the smooth interfacing of database packages")
- (description "The package enables a simple unified interface to several
-annotation packages each of which has its own schema by taking advantage of
-the fact that each of these packages implements a select methods.")
- (license license:artistic2.0)))
-
(define-public r-biovizbase
(package
(name "r-biovizbase")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:12 GMT) Full text and rfc822 format available.Message #92 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 30/50] gnu: r-vsn: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:02 +0200
* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
---
gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 36 ---------------------------------
2 files changed, 36 insertions(+), 36 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d0ebcf8481..05c4896276 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3480,6 +3480,42 @@ dependencies between GO terms can be implemented and applied.")
coding changes and predict coding outcomes.")
(license license:artistic2.0)))
+(define-public r-vsn
+ (package
+ (name "r-vsn")
+ (version "3.58.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "vsn" version))
+ (sha256
+ (base32
+ "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-biobase" ,r-biobase)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-lattice" ,r-lattice)
+ ("r-limma" ,r-limma)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
+ (synopsis "Variance stabilization and calibration for microarray data")
+ (description
+ "The package implements a method for normalising microarray intensities,
+and works for single- and multiple-color arrays. It can also be used for data
+from other technologies, as long as they have similar format. The method uses
+a robust variant of the maximum-likelihood estimator for an
+additive-multiplicative error model and affine calibration. The model
+incorporates data calibration step (a.k.a. normalization), a model for the
+dependence of the variance on the mean intensity and a variance stabilizing
+data transformation. Differences between transformed intensities are
+analogous to \"normalized log-ratios\". However, in contrast to the latter,
+their variance is independent of the mean, and they are usually more sensitive
+and specific in detecting differential transcription.")
+ (license license:artistic2.0)))
+
(define-public r-xvector
(package
(name "r-xvector")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7256df3f83..600c2ca81e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8934,42 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has
previously been used in XCMS.")
(license license:artistic2.0)))
-(define-public r-vsn
- (package
- (name "r-vsn")
- (version "3.58.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "vsn" version))
- (sha256
- (base32
- "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-ggplot2" ,r-ggplot2)
- ("r-lattice" ,r-lattice)
- ("r-limma" ,r-limma)))
- (native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
- (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
- (synopsis "Variance stabilization and calibration for microarray data")
- (description
- "The package implements a method for normalising microarray intensities,
-and works for single- and multiple-color arrays. It can also be used for data
-from other technologies, as long as they have similar format. The method uses
-a robust variant of the maximum-likelihood estimator for an
-additive-multiplicative error model and affine calibration. The model
-incorporates data calibration step (a.k.a. normalization), a model for the
-dependence of the variance on the mean intensity and a variance stabilizing
-data transformation. Differences between transformed intensities are
-analogous to \"normalized log-ratios\". However, in contrast to the latter,
-their variance is independent of the mean, and they are usually more sensitive
-and specific in detecting differential transcription.")
- (license license:artistic2.0)))
-
(define-public r-ensembldb
(package
(name "r-ensembldb")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:12 GMT) Full text and rfc822 format available.Message #95 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 31/50] gnu: r-biovizbase: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:03 +0200
* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...
* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
---
gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 42 ---------------------------------
2 files changed, 42 insertions(+), 42 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 05c4896276..7439ad96da 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2044,6 +2044,48 @@ matching algorithms, and other utilities, for fast manipulation of large
biological sequences or sets of sequences.")
(license license:artistic2.0)))
+(define-public r-biovizbase
+ (package
+ (name "r-biovizbase")
+ (version "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biovizBase" version))
+ (sha256
+ (base32
+ "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))
+ (properties `((upstream-name . "biovizBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dichromat" ,r-dichromat)
+ ("r-ensembldb" ,r-ensembldb)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hmisc" ,r-hmisc)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rlang" ,r-rlang)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/biovizBase")
+ (synopsis "Basic graphic utilities for visualization of genomic data")
+ (description
+ "The biovizBase package is designed to provide a set of utilities, color
+schemes and conventions for genomic data. It serves as the base for various
+high-level packages for biological data visualization. This saves development
+effort and encourages consistency.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome
(package
(name "r-bsgenome")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 600c2ca81e..e6692ece0c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8979,48 +8979,6 @@ chromosome region or transcript models of lincRNA genes.")
;; No version specified
(license license:lgpl3+)))
-(define-public r-biovizbase
- (package
- (name "r-biovizbase")
- (version "1.38.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "biovizBase" version))
- (sha256
- (base32
- "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))
- (properties `((upstream-name . "biovizBase")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-dichromat" ,r-dichromat)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-hmisc" ,r-hmisc)
- ("r-iranges" ,r-iranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rlang" ,r-rlang)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (home-page "https://bioconductor.org/packages/biovizBase")
- (synopsis "Basic graphic utilities for visualization of genomic data")
- (description
- "The biovizBase package is designed to provide a set of utilities, color
-schemes and conventions for genomic data. It serves as the base for various
-high-level packages for biological data visualization. This saves development
-effort and encourages consistency.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:13 GMT) Full text and rfc822 format available.Message #98 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 32/50] gnu: r-ensembldb: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:04 +0200
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 45 ---------------------------------
2 files changed, 45 insertions(+), 45 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7439ad96da..7e86af7d21 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2398,6 +2398,51 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and
CAGE.")
(license license:gpl2+)))
+(define-public r-ensembldb
+ (package
+ (name "r-ensembldb")
+ (version "2.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ensembldb" version))
+ (sha256
+ (base32
+ "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-curl" ,r-curl)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/jotsetung/ensembldb")
+ (synopsis "Utilities to create and use Ensembl-based annotation databases")
+ (description
+ "The package provides functions to create and use transcript-centric
+annotation databases/packages. The annotation for the databases are directly
+fetched from Ensembl using their Perl API. The functionality and data is
+similar to that of the TxDb packages from the @code{GenomicFeatures} package,
+but, in addition to retrieve all gene/transcript models and annotations from
+the database, the @code{ensembldb} package also provides a filter framework
+allowing to retrieve annotations for specific entries like genes encoded on a
+chromosome region or transcript models of lincRNA genes.")
+ ;; No version specified
+ (license license:lgpl3+)))
+
(define-public r-fastseg
(package
(name "r-fastseg")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e6692ece0c..baef88cd2e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8934,51 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has
previously been used in XCMS.")
(license license:artistic2.0)))
-(define-public r-ensembldb
- (package
- (name "r-ensembldb")
- (version "2.14.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ensembldb" version))
- (sha256
- (base32
- "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-curl" ,r-curl)
- ("r-dbi" ,r-dbi)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/jotsetung/ensembldb")
- (synopsis "Utilities to create and use Ensembl-based annotation databases")
- (description
- "The package provides functions to create and use transcript-centric
-annotation databases/packages. The annotation for the databases are directly
-fetched from Ensembl using their Perl API. The functionality and data is
-similar to that of the TxDb packages from the @code{GenomicFeatures} package,
-but, in addition to retrieve all gene/transcript models and annotations from
-the database, the @code{ensembldb} package also provides a filter framework
-allowing to retrieve annotations for specific entries like genes encoded on a
-chromosome region or transcript models of lincRNA genes.")
- ;; No version specified
- (license license:lgpl3+)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:13 GMT) Full text and rfc822 format available.Message #101 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 33/50] gnu: r-mzr: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:05 +0200
* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
---
gnu/packages/bioconductor.scm | 62 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 61 --------------------------------
2 files changed, 62 insertions(+), 61 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7e86af7d21..5ceffd7b4d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -36,6 +36,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
+ #:use-module (gnu packages boost)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
#:use-module (gnu packages gcc)
@@ -3051,6 +3052,67 @@ mzIdentML files with the drawback of having less pretty output than a vendor
specific parser.")
(license license:gpl2+)))
+(define-public r-mzr
+ (package
+ (name "r-mzr")
+ (version "2.24.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "mzR" version))
+ (sha256
+ (base32
+ "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "src/boost")
+ #t))))
+ (properties `((upstream-name . "mzR")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-boost
+ (lambda _
+ (substitute* "src/Makevars"
+ (("\\./boost/libs.*") "")
+ ;; This is to avoid having a plain directory on the list of
+ ;; libraries to link.
+ (("\\(RHDF5_LIBS\\)" match)
+ (string-append match "/libhdf5.a"))
+ (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
+ (("\\ARCH_OBJS=" line)
+ (string-append line
+ "\nBOOST_LIBS=-lboost_system -lboost_regex \
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
+ #t)))))
+ (inputs
+ `(;; Our default boost package won't work here, unfortunately, even with
+ ;; mzR version 2.24.1.
+ ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-ncdf4" ,r-ncdf4)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhdf5lib" ,r-rhdf5lib)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/sneumann/mzR/")
+ (synopsis "Parser for mass spectrometry data files")
+ (description
+ "The mzR package provides a unified API to the common file formats and
+parsers available for mass spectrometry data. It comes with a wrapper for the
+ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
+The package contains the original code written by the ISB, and a subset of the
+proteowizard library for mzML and mzIdentML. The netCDF reading code has
+previously been used in XCMS.")
+ (license license:artistic2.0)))
+
(define-public r-organismdbi
(package
(name "r-organismdbi")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index baef88cd2e..a6321a179a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8873,67 +8873,6 @@ trait.")
proteomics packages.")
(license license:artistic2.0)))
-(define-public r-mzr
- (package
- (name "r-mzr")
- (version "2.24.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "mzR" version))
- (sha256
- (base32
- "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- (delete-file-recursively "src/boost")
- #t))))
- (properties `((upstream-name . "mzR")))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'use-system-boost
- (lambda _
- (substitute* "src/Makevars"
- (("\\./boost/libs.*") "")
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\(RHDF5_LIBS\\)" match)
- (string-append match "/libhdf5.a"))
- (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
- (("\\ARCH_OBJS=" line)
- (string-append line
- "\nBOOST_LIBS=-lboost_system -lboost_regex \
--lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
- #t)))))
- (inputs
- `(;; Our default boost package won't work here, unfortunately, even with
- ;; mzR version 2.24.1.
- ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
- ("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-ncdf4" ,r-ncdf4)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rcpp" ,r-rcpp)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/sneumann/mzR/")
- (synopsis "Parser for mass spectrometry data files")
- (description
- "The mzR package provides a unified API to the common file formats and
-parsers available for mass spectrometry data. It comes with a wrapper for the
-ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
-The package contains the original code written by the ISB, and a subset of the
-proteowizard library for mzML and mzIdentML. The netCDF reading code has
-previously been used in XCMS.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:14 GMT) Full text and rfc822 format available.Message #104 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 34/50] gnu: r-protgenerics: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:06 +0200
* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
---
gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
gnu/packages/bioinformatics.scm | 20 --------------------
2 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5ceffd7b4d..a9365a4018 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3175,6 +3175,26 @@ the results is also provided. All PCA methods make use of the same data
structure (pcaRes) to provide a common interface to the PCA results.")
(license license:gpl3+)))
+(define-public r-protgenerics
+ (package
+ (name "r-protgenerics")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ProtGenerics" version))
+ (sha256
+ (base32
+ "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))
+ (properties `((upstream-name . "ProtGenerics")))
+ (build-system r-build-system)
+ (home-page "https://github.com/lgatto/ProtGenerics")
+ (synopsis "S4 generic functions for proteomics infrastructure")
+ (description
+ "This package provides S4 generic functions needed by Bioconductor
+proteomics packages.")
+ (license license:artistic2.0)))
+
(define-public r-rbgl
(package
(name "r-rbgl")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a6321a179a..6120cb6804 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8853,26 +8853,6 @@ for analyzing gene-level association tests in meta-analyses for binary
trait.")
(license license:gpl3)))
-(define-public r-protgenerics
- (package
- (name "r-protgenerics")
- (version "1.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ProtGenerics" version))
- (sha256
- (base32
- "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))
- (properties `((upstream-name . "ProtGenerics")))
- (build-system r-build-system)
- (home-page "https://github.com/lgatto/ProtGenerics")
- (synopsis "S4 generic functions for proteomics infrastructure")
- (description
- "This package provides S4 generic functions needed by Bioconductor
-proteomics packages.")
- (license license:artistic2.0)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:14 GMT) Full text and rfc822 format available.Message #107 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 35/50] gnu: r-sva: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:07 +0200
* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
---
gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a9365a4018..a7b1c63b56 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3524,6 +3524,37 @@ typically represent genomic ranges of interest and the columns represent
samples.")
(license license:artistic2.0)))
+(define-public r-sva
+ (package
+ (name "r-sva")
+ (version "3.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "sva" version))
+ (sha256
+ (base32
+ "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-edger" ,r-edger)
+ ("r-genefilter" ,r-genefilter)
+ ("r-mgcv" ,r-mgcv)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-limma" ,r-limma)))
+ (home-page "https://bioconductor.org/packages/sva")
+ (synopsis "Surrogate variable analysis")
+ (description
+ "This package contains functions for removing batch effects and other
+unwanted variation in high-throughput experiment. It also contains functions
+for identifying and building surrogate variables for high-dimensional data
+sets. Surrogate variables are covariates constructed directly from
+high-dimensional data like gene expression/RNA sequencing/methylation/brain
+imaging data that can be used in subsequent analyses to adjust for unknown,
+unmodeled, or latent sources of noise.")
+ (license license:artistic2.0)))
+
(define-public r-systempiper
(package
(name "r-systempiper")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6120cb6804..2cc41b7e98 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8790,37 +8790,6 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and
TAB-Seq.")
(license license:artistic2.0)))
-(define-public r-sva
- (package
- (name "r-sva")
- (version "3.38.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "sva" version))
- (sha256
- (base32
- "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-edger" ,r-edger)
- ("r-genefilter" ,r-genefilter)
- ("r-mgcv" ,r-mgcv)
- ("r-biocparallel" ,r-biocparallel)
- ("r-matrixstats" ,r-matrixstats)
- ("r-limma" ,r-limma)))
- (home-page "https://bioconductor.org/packages/sva")
- (synopsis "Surrogate variable analysis")
- (description
- "This package contains functions for removing batch effects and other
-unwanted variation in high-throughput experiment. It also contains functions
-for identifying and building surrogate variables for high-dimensional data
-sets. Surrogate variables are covariates constructed directly from
-high-dimensional data like gene expression/RNA sequencing/methylation/brain
-imaging data that can be used in subsequent analyses to adjust for unknown,
-unmodeled, or latent sources of noise.")
- (license license:artistic2.0)))
-
(define-public r-raremetals2
(package
(name "r-raremetals2")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:14 GMT) Full text and rfc822 format available.Message #110 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 36/50] gnu: r-motifrg: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:08 +0200
* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...
* gnu/packages/bioconductor.scm (r-motifrg): ...to here.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 27 ---------------------------
2 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a7b1c63b56..47a245b4f5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2924,6 +2924,33 @@ and the assessment of differential expression. The analysis methods apply to
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
+(define-public r-motifrg
+ (package
+ (name "r-motifrg")
+ (version "1.31.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "motifRG" version))
+ (sha256
+ (base32
+ "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
+ (properties `((upstream-name . "motifRG")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-iranges" ,r-iranges)
+ ("r-seqlogo" ,r-seqlogo)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/motifRG")
+ (synopsis "Discover motifs in high throughput sequencing data")
+ (description
+ "This package provides tools for discriminative motif discovery in high
+throughput genetic sequencing data sets using regression methods.")
+ (license license:artistic2.0)))
+
(define-public r-msnbase
(package
(name "r-msnbase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2cc41b7e98..e2000ccb68 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,33 +7872,6 @@ plots the corresponding sequence logo as introduced by Schneider and
Stephens (1990).")
(license license:lgpl2.0+)))
-(define-public r-motifrg
- (package
- (name "r-motifrg")
- (version "1.31.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "motifRG" version))
- (sha256
- (base32
- "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
- (properties `((upstream-name . "motifRG")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-iranges" ,r-iranges)
- ("r-seqlogo" ,r-seqlogo)
- ("r-xvector" ,r-xvector)))
- (home-page "https://bioconductor.org/packages/motifRG")
- (synopsis "Discover motifs in high throughput sequencing data")
- (description
- "This package provides tools for discriminative motif discovery in high
-throughput genetic sequencing data sets using regression methods.")
- (license license:artistic2.0)))
-
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:15 GMT) Full text and rfc822 format available.Message #113 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 37/50] gnu: r-seqlogo: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:09 +0200
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...
* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
---
gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 23 -----------------------
2 files changed, 23 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 47a245b4f5..c58c5af5d6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3447,6 +3447,29 @@ differential expression analysis, RNAseq data and related problems.")
;; Any version of the LGPL
(license license:lgpl3+)))
+(define-public r-seqlogo
+ (package
+ (name "r-seqlogo")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "seqLogo" version))
+ (sha256
+ (base32
+ "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))
+ (properties `((upstream-name . "seqLogo")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/seqLogo")
+ (synopsis "Sequence logos for DNA sequence alignments")
+ (description
+ "seqLogo takes the position weight matrix of a DNA sequence motif and
+plots the corresponding sequence logo as introduced by Schneider and
+Stephens (1990).")
+ (license license:lgpl2.0+)))
+
(define-public r-seqpattern
(package
(name "r-seqpattern")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e2000ccb68..9ba818d581 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,29 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-seqlogo
- (package
- (name "r-seqlogo")
- (version "1.56.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "seqLogo" version))
- (sha256
- (base32
- "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))
- (properties `((upstream-name . "seqLogo")))
- (build-system r-build-system)
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/seqLogo")
- (synopsis "Sequence logos for DNA sequence alignments")
- (description
- "seqLogo takes the position weight matrix of a DNA sequence motif and
-plots the corresponding sequence logo as introduced by Schneider and
-Stephens (1990).")
- (license license:lgpl2.0+)))
-
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:15 GMT) Full text and rfc822 format available.Message #116 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 38/50] gnu: r-zlibbioc: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:10 +0200
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...
* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
---
gnu/packages/bioconductor.scm | 19 +++++++++++++++++++
gnu/packages/bioinformatics.scm | 19 -------------------
2 files changed, 19 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c58c5af5d6..e720d7bf6a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3802,6 +3802,25 @@ and specific in detecting differential transcription.")
\"externally\" (behind an R external pointer, or on disk).")
(license license:artistic2.0)))
+ (define-public r-zlibbioc
+ (package
+ (name "r-zlibbioc")
+ (version "1.36.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "zlibbioc" version))
+ (sha256
+ (base32
+ "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))
+ (properties
+ `((upstream-name . "zlibbioc")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/zlibbioc")
+ (synopsis "Provider for zlib-1.2.5 to R packages")
+ (description "This package uses the source code of zlib-1.2.5 to create
+libraries for systems that do not have these available via other means.")
+ (license license:artistic2.0)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9ba818d581..39c437f4a2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,25 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-zlibbioc
- (package
- (name "r-zlibbioc")
- (version "1.36.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "zlibbioc" version))
- (sha256
- (base32
- "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))
- (properties
- `((upstream-name . "zlibbioc")))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/zlibbioc")
- (synopsis "Provider for zlib-1.2.5 to R packages")
- (description "This package uses the source code of zlib-1.2.5 to create
-libraries for systems that do not have these available via other means.")
- (license license:artistic2.0)))
-
(define-public r-r4rna
(package
(name "r-r4rna")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:15 GMT) Full text and rfc822 format available.Message #119 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 29/50] gnu: r-affyio: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:01 +0200
* gnu/packages/bioinformatics.scm (r-affyio): Move from here...
* gnu/packages/bioconductor.scm (r-affyio): ...to here.
---
gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 24 ------------------------
2 files changed, 24 insertions(+), 24 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c63d39dc9c..d0ebcf8481 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1694,6 +1694,30 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
to streamline the more common analyses that a Biostatistician might see.")
(license license:artistic2.0)))
+(define-public r-affyio
+ (package
+ (name "r-affyio")
+ (version "1.60.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affyio" version))
+ (sha256
+ (base32
+ "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/bmbolstad/affyio")
+ (synopsis "Tools for parsing Affymetrix data files")
+ (description
+ "This package provides routines for parsing Affymetrix data files based
+upon file format information. The primary focus is on accessing the CEL and
+CDF file formats.")
+ (license license:lgpl2.0+)))
+
(define-public r-affxparser
(package
(name "r-affxparser")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1c90700c95..7256df3f83 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8934,30 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has
previously been used in XCMS.")
(license license:artistic2.0)))
-(define-public r-affyio
- (package
- (name "r-affyio")
- (version "1.60.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "affyio" version))
- (sha256
- (base32
- "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-zlibbioc" ,r-zlibbioc)))
- (inputs
- `(("zlib" ,zlib)))
- (home-page "https://github.com/bmbolstad/affyio")
- (synopsis "Tools for parsing Affymetrix data files")
- (description
- "This package provides routines for parsing Affymetrix data files based
-upon file format information. The primary focus is on accessing the CEL and
-CDF file formats.")
- (license license:lgpl2.0+)))
-
(define-public r-vsn
(package
(name "r-vsn")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:16 GMT) Full text and rfc822 format available.Message #122 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 41/50] gnu: r-rcas: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:13 +0200
* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
---
gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 49 ---------------------------------
2 files changed, 49 insertions(+), 49 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 99607ba564..1d38fa1c05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3307,6 +3307,55 @@ proteomics packages.")
the graph algorithms contained in the Boost library.")
(license license:artistic2.0)))
+(define-public r-rcas
+ (package
+ (name "r-rcas")
+ (version "1.16.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RCAS" version))
+ (sha256
+ (base32
+ "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))
+ (properties `((upstream-name . "RCAS")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-cowplot" ,r-cowplot)
+ ("r-data-table" ,r-data-table)
+ ("r-dt" ,r-dt)
+ ("r-genomation" ,r-genomation)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggseqlogo" ,r-ggseqlogo)
+ ("r-gprofiler2" ,r-gprofiler2)
+ ("r-iranges" ,r-iranges)
+ ("r-pbapply" ,r-pbapply)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-plotly" ,r-plotly)
+ ("r-plotrix" ,r-plotrix)
+ ("r-proxy" ,r-proxy)
+ ("r-ranger" ,r-ranger)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-s4vectors" ,r-s4vectors)
+ ("pandoc" ,pandoc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (synopsis "RNA-centric annotation system")
+ (description
+ "RCAS aims to be a standalone RNA-centric annotation system that provides
+intuitive reports and publication-ready graphics. This package provides the R
+library implementing most of the pipeline's features.")
+ (home-page "https://github.com/BIMSBbioinfo/RCAS")
+ (license license:artistic2.0)))
+
(define-public r-regioner
(package
(name "r-regioner")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ae61ecae74..a1ee4b6772 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,55 +7872,6 @@ including VCF header and contents in RDF and JSON.")
secondary structure and comparative analysis in R.")
(license license:gpl3+)))
-(define-public r-rcas
- (package
- (name "r-rcas")
- (version "1.16.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "RCAS" version))
- (sha256
- (base32
- "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))
- (properties `((upstream-name . "RCAS")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-cowplot" ,r-cowplot)
- ("r-data-table" ,r-data-table)
- ("r-dt" ,r-dt)
- ("r-genomation" ,r-genomation)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggseqlogo" ,r-ggseqlogo)
- ("r-gprofiler2" ,r-gprofiler2)
- ("r-iranges" ,r-iranges)
- ("r-pbapply" ,r-pbapply)
- ("r-pheatmap" ,r-pheatmap)
- ("r-plotly" ,r-plotly)
- ("r-plotrix" ,r-plotrix)
- ("r-proxy" ,r-proxy)
- ("r-ranger" ,r-ranger)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-s4vectors" ,r-s4vectors)
- ("pandoc" ,pandoc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (synopsis "RNA-centric annotation system")
- (description
- "RCAS aims to be a standalone RNA-centric annotation system that provides
-intuitive reports and publication-ready graphics. This package provides the R
-library implementing most of the pipeline's features.")
- (home-page "https://github.com/BIMSBbioinfo/RCAS")
- (license license:artistic2.0)))
-
(define-public rcas-web
(package
(name "rcas-web")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:16 GMT) Full text and rfc822 format available.Message #125 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 42/50] gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:14 +0200
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
---
gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 45 ---------------------------------
2 files changed, 45 insertions(+), 45 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1d38fa1c05..7c471c7375 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3013,6 +3013,51 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
throughput genetic sequencing data sets using regression methods.")
(license license:artistic2.0)))
+(define-public r-mutationalpatterns
+ (package
+ (name "r-mutationalpatterns")
+ (version "3.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MutationalPatterns" version))
+ (sha256
+ (base32
+ "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ;; These two packages are suggested packages
+ ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-cowplot" ,r-cowplot)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggalluvial" ,r-ggalluvial)
+ ("r-ggdendro" ,r-ggdendro)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-magrittr" ,r-magrittr)
+ ("r-nmf" ,r-nmf)
+ ("r-pracma" ,r-pracma)
+ ("r-purrr" ,r-purrr)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/MutationalPatterns/")
+ (synopsis "Extract and visualize mutational patterns in genomic data")
+ (description "This package provides an extensive toolset for the
+characterization and visualization of a wide range of mutational patterns
+in SNV base substitution data.")
+ (license license:expat)))
+
(define-public r-msnbase
(package
(name "r-msnbase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a1ee4b6772..b5b2cc2f6b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7923,51 +7923,6 @@ secondary structure and comparative analysis in R.")
@dfn{RNA-centric annotation system} (RCAS).")
(license license:agpl3+)))
-(define-public r-mutationalpatterns
- (package
- (name "r-mutationalpatterns")
- (version "3.0.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "MutationalPatterns" version))
- (sha256
- (base32
- "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))
- (build-system r-build-system)
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ;; These two packages are suggested packages
- ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-cowplot" ,r-cowplot)
- ("r-dplyr" ,r-dplyr)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggalluvial" ,r-ggalluvial)
- ("r-ggdendro" ,r-ggdendro)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-magrittr" ,r-magrittr)
- ("r-nmf" ,r-nmf)
- ("r-pracma" ,r-pracma)
- ("r-purrr" ,r-purrr)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-variantannotation" ,r-variantannotation)))
- (home-page "https://bioconductor.org/packages/MutationalPatterns/")
- (synopsis "Extract and visualize mutational patterns in genomic data")
- (description "This package provides an extensive toolset for the
-characterization and visualization of a wide range of mutational patterns
-in SNV base substitution data.")
- (license license:expat)))
-
(define-public r-chipkernels
(let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
(revision "1"))
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:17 GMT) Full text and rfc822 format available.Message #128 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 43/50] gnu: r-tximport: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:15 +0200
* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
---
gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 24 ------------------------
2 files changed, 24 insertions(+), 24 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7c471c7375..30d4844ae4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3848,6 +3848,30 @@ dependencies between GO terms can be implemented and applied.")
;; Any version of the LGPL applies.
(license license:lgpl2.1+)))
+(define-public r-tximport
+ (package
+ (name "r-tximport")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tximport" version))
+ (sha256
+ (base32
+ "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/tximport")
+ (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
+ (description
+ "This package provides tools to import transcript-level abundance,
+estimated counts and transcript lengths, and to summarize them into matrices
+for use with downstream gene-level analysis packages. Average transcript
+length, weighted by sample-specific transcript abundance estimates, is
+provided as a matrix which can be used as an offset for different expression
+of gene-level counts.")
+ (license license:gpl2+)))
+
(define-public r-variantannotation
(package
(name "r-variantannotation")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b5b2cc2f6b..83d6797809 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7990,30 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription
factors bound at the specific regions.")
(license license:gpl2+)))
-(define-public r-tximport
- (package
- (name "r-tximport")
- (version "1.18.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "tximport" version))
- (sha256
- (base32
- "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))
- (build-system r-build-system)
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/tximport")
- (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
- (description
- "This package provides tools to import transcript-level abundance,
-estimated counts and transcript lengths, and to summarize them into matrices
-for use with downstream gene-level analysis packages. Average transcript
-length, weighted by sample-specific transcript abundance estimates, is
-provided as a matrix which can be used as an offset for different expression
-of gene-level counts.")
- (license license:gpl2+)))
-
(define-public r-rhdf5filters
(package
(name "r-rhdf5filters")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:17 GMT) Full text and rfc822 format available.Message #131 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 44/50] gnu: r-rhdf5filters: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:16 +0200
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 26 --------------------------
2 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 30d4844ae4..8695f13ed8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3482,6 +3482,32 @@ reports together for a particular project that can be viewed in a web
browser.")
(license license:artistic2.0)))
+(define-public r-rhdf5filters
+ (package
+ (name "r-rhdf5filters")
+ (version "1.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rhdf5filters" version))
+ (sha256
+ (base32
+ "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz"))))
+ (properties `((upstream-name . "rhdf5filters")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rhdf5lib" ,r-rhdf5lib)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/grimbough/rhdf5filters")
+ (synopsis "HDF5 compression filters")
+ (description
+ "This package provides a collection of compression filters for use with
+HDF5 datasets.")
+ (license license:bsd-2)))
+
(define-public r-rsamtools
(package
(name "r-rsamtools")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 83d6797809..2907d65b38 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7990,32 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription
factors bound at the specific regions.")
(license license:gpl2+)))
-(define-public r-rhdf5filters
- (package
- (name "r-rhdf5filters")
- (version "1.2.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "rhdf5filters" version))
- (sha256
- (base32
- "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz"))))
- (properties `((upstream-name . "rhdf5filters")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-rhdf5lib" ,r-rhdf5lib)))
- (inputs
- `(("zlib" ,zlib)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/grimbough/rhdf5filters")
- (synopsis "HDF5 compression filters")
- (description
- "This package provides a collection of compression filters for use with
-HDF5 datasets.")
- (license license:bsd-2)))
-
(define-public r-rhdf5
(package
(name "r-rhdf5")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:17 GMT) Full text and rfc822 format available.Message #134 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 45/50] gnu: r-annotationfilter: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:17 +0200
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 26 --------------------------
2 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8695f13ed8..87b879ad94 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1804,6 +1804,32 @@ microarrays.")
annotation data packages using SQLite data storage.")
(license license:artistic2.0)))
+(define-public r-annotationfilter
+ (package
+ (name "r-annotationfilter")
+ (version "1.14.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationFilter" version))
+ (sha256
+ (base32
+ "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))
+ (properties
+ `((upstream-name . "AnnotationFilter")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomicranges" ,r-genomicranges)
+ ("r-lazyeval" ,r-lazyeval)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/Bioconductor/AnnotationFilter")
+ (synopsis "Facilities for filtering Bioconductor annotation resources")
+ (description
+ "This package provides classes and other infrastructure to implement
+filters for manipulating Bioconductor annotation resources. The filters are
+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
+ (license license:artistic2.0)))
+
(define-public r-annotationforge
(package
(name "r-annotationforge")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2907d65b38..7ad51d3518 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8029,32 +8029,6 @@ package, and for letting R applications work on datasets that are larger than
the available RAM.")
(license license:artistic2.0)))
-(define-public r-annotationfilter
- (package
- (name "r-annotationfilter")
- (version "1.14.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "AnnotationFilter" version))
- (sha256
- (base32
- "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))
- (properties
- `((upstream-name . "AnnotationFilter")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-genomicranges" ,r-genomicranges)
- ("r-lazyeval" ,r-lazyeval)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/Bioconductor/AnnotationFilter")
- (synopsis "Facilities for filtering Bioconductor annotation resources")
- (description
- "This package provides classes and other infrastructure to implement
-filters for manipulating Bioconductor annotation resources. The filters are
-used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
- (license license:artistic2.0)))
-
(define-public emboss
(package
(name "emboss")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:18 GMT) Full text and rfc822 format available.Message #137 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 46/50] gnu: r-rhdf5: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:18 +0200
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
---
gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 39 ---------------------------------
2 files changed, 39 insertions(+), 39 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 87b879ad94..d027a24bf3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3508,6 +3508,45 @@ reports together for a particular project that can be viewed in a web
browser.")
(license license:artistic2.0)))
+(define-public r-rhdf5
+ (package
+ (name "r-rhdf5")
+ (version "2.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rhdf5" version))
+ (sha256
+ (base32
+ "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-linking
+ (lambda _
+ (substitute* "src/Makevars"
+ ;; This is to avoid having a plain directory on the list of
+ ;; libraries to link.
+ (("\\(RHDF5_LIBS\\)" match)
+ (string-append match "/libhdf5.a")))
+ #t)))))
+ (propagated-inputs
+ `(("r-rhdf5filters" ,r-rhdf5filters)
+ ("r-rhdf5lib" ,r-rhdf5lib)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/rhdf5")
+ (synopsis "HDF5 interface to R")
+ (description
+ "This R/Bioconductor package provides an interface between HDF5 and R.
+HDF5's main features are the ability to store and access very large and/or
+complex datasets and a wide variety of metadata on mass storage (disk) through
+a completely portable file format. The rhdf5 package is thus suited for the
+exchange of large and/or complex datasets between R and other software
+package, and for letting R applications work on datasets that are larger than
+the available RAM.")
+ (license license:artistic2.0)))
+
(define-public r-rhdf5filters
(package
(name "r-rhdf5filters")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7ad51d3518..ef0d7b3007 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7990,45 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription
factors bound at the specific regions.")
(license license:gpl2+)))
-(define-public r-rhdf5
- (package
- (name "r-rhdf5")
- (version "2.34.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "rhdf5" version))
- (sha256
- (base32
- "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-linking
- (lambda _
- (substitute* "src/Makevars"
- ;; This is to avoid having a plain directory on the list of
- ;; libraries to link.
- (("\\(RHDF5_LIBS\\)" match)
- (string-append match "/libhdf5.a")))
- #t)))))
- (propagated-inputs
- `(("r-rhdf5filters" ,r-rhdf5filters)
- ("r-rhdf5lib" ,r-rhdf5lib)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/rhdf5")
- (synopsis "HDF5 interface to R")
- (description
- "This R/Bioconductor package provides an interface between HDF5 and R.
-HDF5's main features are the ability to store and access very large and/or
-complex datasets and a wide variety of metadata on mass storage (disk) through
-a completely portable file format. The rhdf5 package is thus suited for the
-exchange of large and/or complex datasets between R and other software
-package, and for letting R applications work on datasets that are larger than
-the available RAM.")
- (license license:artistic2.0)))
-
(define-public emboss
(package
(name "emboss")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:18 GMT) Full text and rfc822 format available.Message #140 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 47/50] gnu: r-chipseq: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:19 +0200
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 26 --------------------------
2 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d027a24bf3..f224a5ecb4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2206,6 +2206,32 @@ genome data packages and support for efficient SNP representation.")
analysis.")
(license license:artistic2.0)))
+(define-public r-chipseq
+ (package
+ (name "r-chipseq")
+ (version "1.40.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "chipseq" version))
+ (sha256
+ (base32
+ "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shortread" ,r-shortread)))
+ (home-page "https://bioconductor.org/packages/chipseq")
+ (synopsis "Package for analyzing ChIPseq data")
+ (description
+ "This package provides tools for processing short read data from ChIPseq
+experiments.")
+ (license license:artistic2.0)))
+
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef0d7b3007..3ee3d9d4f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
-(define-public r-chipseq
- (package
- (name "r-chipseq")
- (version "1.40.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "chipseq" version))
- (sha256
- (base32
- "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shortread" ,r-shortread)))
- (home-page "https://bioconductor.org/packages/chipseq")
- (synopsis "Package for analyzing ChIPseq data")
- (description
- "This package provides tools for processing short read data from ChIPseq
-experiments.")
- (license license:artistic2.0)))
-
(define-public r-copyhelper
(package
(name "r-copyhelper")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:19 GMT) Full text and rfc822 format available.Message #143 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 48/50] gnu: r-copyhelper: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:20 +0200
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
---
gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 26 --------------------------
2 files changed, 24 insertions(+), 26 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f224a5ecb4..eee1561c1b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -999,6 +999,30 @@ from Illumina 450k methylation arrays.")
chromstaR package.")
(license license:gpl3)))
+(define-public r-copyhelper
+ (package
+ (name "r-copyhelper")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
+ (sha256
+ (base32
+ "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+ (properties `((upstream-name . "CopyhelpeR")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/CopyhelpeR/")
+ (synopsis "Helper files for CopywriteR")
+ (description
+ "This package contains the helper files that are required to run the
+Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
+and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
+mm10. In addition, it contains a blacklist filter to remove regions that
+display copy number variation. Files are stored as GRanges objects from the
+GenomicRanges Bioconductor package.")
+ (license license:gpl2)))
+
(define-public r-genelendatabase
(package
(name "r-genelendatabase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3ee3d9d4f3..2acca0c055 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
-(define-public r-copyhelper
- (package
- (name "r-copyhelper")
- (version "1.6.0")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://bioconductor.org/packages/release/"
- "data/experiment/src/contrib/CopyhelpeR_"
- version ".tar.gz"))
- (sha256
- (base32
- "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
- (properties `((upstream-name . "CopyhelpeR")))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/CopyhelpeR/")
- (synopsis "Helper files for CopywriteR")
- (description
- "This package contains the helper files that are required to run the
-Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
-and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
-mm10. In addition, it contains a blacklist filter to remove regions that
-display copy number variation. Files are stored as GRanges objects from the
-GenomicRanges Bioconductor package.")
- (license license:gpl2)))
-
(define-public r-copywriter
(package
(name "r-copywriter")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:19 GMT) Full text and rfc822 format available.Message #146 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 50/50] gnu: r-methylkit: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:22 +0200
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
---
gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 47 ---------------------------------
2 files changed, 47 insertions(+), 47 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fe91fd486f..54a6afcf3d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3102,6 +3102,53 @@ and the assessment of differential expression. The analysis methods apply to
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
+(define-public r-methylkit
+ (package
+ (name "r-methylkit")
+ (version "1.16.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "methylKit" version))
+ (sha256
+ (base32
+ "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
+ (properties `((upstream-name . "methylKit")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-emdbook" ,r-emdbook)
+ ("r-fastseg" ,r-fastseg)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-limma" ,r-limma)
+ ("r-mclust" ,r-mclust)
+ ("r-mgcv" ,r-mgcv)
+ ("r-qvalue" ,r-qvalue)
+ ("r-r-utils" ,r-r-utils)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://github.com/al2na/methylKit")
+ (synopsis
+ "DNA methylation analysis from high-throughput bisulfite sequencing results")
+ (description
+ "MethylKit is an R package for DNA methylation analysis and annotation
+from high-throughput bisulfite sequencing. The package is designed to deal
+with sequencing data from @dfn{Reduced representation bisulfite
+sequencing} (RRBS) and its variants, but also target-capture methods and whole
+genome bisulfite sequencing. It also has functions to analyze base-pair
+resolution 5hmC data from experimental protocols such as oxBS-Seq and
+TAB-Seq.")
+ (license license:artistic2.0)))
+
(define-public r-motifrg
(package
(name "r-motifrg")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 79146f915f..48b521f755 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,53 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
-(define-public r-methylkit
- (package
- (name "r-methylkit")
- (version "1.16.1")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "methylKit" version))
- (sha256
- (base32
- "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
- (properties `((upstream-name . "methylKit")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-emdbook" ,r-emdbook)
- ("r-fastseg" ,r-fastseg)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-limma" ,r-limma)
- ("r-mclust" ,r-mclust)
- ("r-mgcv" ,r-mgcv)
- ("r-qvalue" ,r-qvalue)
- ("r-r-utils" ,r-r-utils)
- ("r-rcpp" ,r-rcpp)
- ("r-rhtslib" ,r-rhtslib)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
- (home-page "https://github.com/al2na/methylKit")
- (synopsis
- "DNA methylation analysis from high-throughput bisulfite sequencing results")
- (description
- "MethylKit is an R package for DNA methylation analysis and annotation
-from high-throughput bisulfite sequencing. The package is designed to deal
-with sequencing data from @dfn{Reduced representation bisulfite
-sequencing} (RRBS) and its variants, but also target-capture methods and whole
-genome bisulfite sequencing. It also has functions to analyze base-pair
-resolution 5hmC data from experimental protocols such as oxBS-Seq and
-TAB-Seq.")
- (license license:artistic2.0)))
-
(define-public r-raremetals2
(package
(name "r-raremetals2")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:19 GMT) Full text and rfc822 format available.Message #149 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 49/50] gnu: r-copywriter: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:21 +0200
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
---
gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 40 ---------------------------------
2 files changed, 40 insertions(+), 40 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eee1561c1b..fe91fd486f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2295,6 +2295,46 @@ provides a highly flexible way to arrange multiple heatmaps and supports
self-defined annotation graphics.")
(license license:gpl2+)))
+(define-public r-copywriter
+ (package
+ (name "r-copywriter")
+ (version "2.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CopywriteR" version))
+ (sha256
+ (base32
+ "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))
+ (properties `((upstream-name . "CopywriteR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-chipseq" ,r-chipseq)
+ ("r-copyhelper" ,r-copyhelper)
+ ("r-data-table" ,r-data-table)
+ ("r-dnacopy" ,r-dnacopy)
+ ("r-futile-logger" ,r-futile-logger)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/PeeperLab/CopywriteR")
+ (synopsis "Copy number information from targeted sequencing")
+ (description
+ "CopywriteR extracts DNA copy number information from targeted sequencing
+by utilizing off-target reads. It allows for extracting uniformly distributed
+copy number information, can be used without reference, and can be applied to
+sequencing data obtained from various techniques including chromatin
+immunoprecipitation and target enrichment on small gene panels. Thereby,
+CopywriteR constitutes a widely applicable alternative to available copy
+number detection tools.")
+ (license license:gpl2)))
+
(define-public r-deseq
(package
(name "r-deseq")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2acca0c055..79146f915f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,46 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
manipulate and analyze genetic variants.")
(license license:gpl3+)))
-(define-public r-copywriter
- (package
- (name "r-copywriter")
- (version "2.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "CopywriteR" version))
- (sha256
- (base32
- "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))
- (properties `((upstream-name . "CopywriteR")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-chipseq" ,r-chipseq)
- ("r-copyhelper" ,r-copyhelper)
- ("r-data-table" ,r-data-table)
- ("r-dnacopy" ,r-dnacopy)
- ("r-futile-logger" ,r-futile-logger)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)))
- (home-page "https://github.com/PeeperLab/CopywriteR")
- (synopsis "Copy number information from targeted sequencing")
- (description
- "CopywriteR extracts DNA copy number information from targeted sequencing
-by utilizing off-target reads. It allows for extracting uniformly distributed
-copy number information, can be used without reference, and can be applied to
-sequencing data obtained from various techniques including chromatin
-immunoprecipitation and target enrichment on small gene panels. Thereby,
-CopywriteR constitutes a widely applicable alternative to available copy
-number detection tools.")
- (license license:gpl2)))
-
(define-public r-methylkit
(package
(name "r-methylkit")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:20 GMT) Full text and rfc822 format available.Message #152 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:11 +0200
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
---
gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 32 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e720d7bf6a..8e78a2a0ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -39,6 +39,7 @@
#:use-module (gnu packages boost)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages curl)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
@@ -2832,6 +2833,37 @@ Enrichment Analysis} (GSEA).")
the Human Protein Atlas project.")
(license license:artistic2.0)))
+(define-public r-rhtslib
+ (package
+ (name "r-rhtslib")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhtslib" version))
+ (sha256
+ (base32
+ "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
+ (properties `((upstream-name . "Rhtslib")))
+ (build-system r-build-system)
+ ;; Without this a temporary directory ends up in the Rhtslib.so binary,
+ ;; which makes R abort the build.
+ (arguments '(#:configure-flags '("--no-staged-install")))
+ (propagated-inputs
+ `(("curl" ,curl)
+ ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/nhayden/Rhtslib")
+ (synopsis "High-throughput sequencing library as an R package")
+ (description
+ "This package provides the HTSlib C library for high-throughput
+nucleotide sequence analysis. The package is primarily useful to developers
+of other R packages who wish to make use of HTSlib.")
+ (license license:lgpl2.0+)))
+
(define-public r-impute
(package
(name "r-impute")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 39c437f4a2..586efcf21e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,37 +7872,6 @@ including VCF header and contents in RDF and JSON.")
secondary structure and comparative analysis in R.")
(license license:gpl3+)))
-(define-public r-rhtslib
- (package
- (name "r-rhtslib")
- (version "1.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rhtslib" version))
- (sha256
- (base32
- "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
- (properties `((upstream-name . "Rhtslib")))
- (build-system r-build-system)
- ;; Without this a temporary directory ends up in the Rhtslib.so binary,
- ;; which makes R abort the build.
- (arguments '(#:configure-flags '("--no-staged-install")))
- (propagated-inputs
- `(("curl" ,curl)
- ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("pkg-config" ,pkg-config)
- ("r-knitr" ,r-knitr)))
- (home-page "https://github.com/nhayden/Rhtslib")
- (synopsis "High-throughput sequencing library as an R package")
- (description
- "This package provides the HTSlib C library for high-throughput
-nucleotide sequence analysis. The package is primarily useful to developers
-of other R packages who wish to make use of HTSlib.")
- (license license:lgpl2.0+)))
-
(define-public r-bamsignals
(package
(name "r-bamsignals")
--
2.30.1
guix-patches <at> gnu.org:bug#48575; Package guix-patches.
(Fri, 21 May 2021 20:28:20 GMT) Full text and rfc822 format available.Message #155 received at 48575 <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: 48575 <at> debbugs.gnu.org. Cc: zimoun <zimon.toutoune <at> gmail.com> Subject: [PATCH 40/50] gnu: r-bamsignals: Move to (gnu packages bioconductor). Date: Fri, 21 May 2021 22:26:12 +0200
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
---
gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 30 ------------------------------
2 files changed, 30 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8e78a2a0ca..99607ba564 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1904,6 +1904,36 @@ standalone, be utilized in other packages, or be wrapped up in higher-level
classes.")
(license license:gpl2+)))
+(define-public r-bamsignals
+ (package
+ (name "r-bamsignals")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bamsignals" version))
+ (sha256
+ (base32
+ "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/bamsignals")
+ (synopsis "Extract read count signals from bam files")
+ (description
+ "This package efficiently obtains count vectors from indexed bam
+files. It counts the number of nucleotide sequence reads in given genomic
+ranges and it computes reads profiles and coverage profiles. It also handles
+paired-end data.")
+ (license license:gpl2+)))
+
(define-public r-biobase
(package
(name "r-biobase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 586efcf21e..ae61ecae74 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,36 +7872,6 @@ including VCF header and contents in RDF and JSON.")
secondary structure and comparative analysis in R.")
(license license:gpl3+)))
-(define-public r-bamsignals
- (package
- (name "r-bamsignals")
- (version "1.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "bamsignals" version))
- (sha256
- (base32
- "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcpp" ,r-rcpp)
- ("r-rhtslib" ,r-rhtslib)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/bamsignals")
- (synopsis "Extract read count signals from bam files")
- (description
- "This package efficiently obtains count vectors from indexed bam
-files. It counts the number of nucleotide sequence reads in given genomic
-ranges and it computes reads profiles and coverage profiles. It also handles
-paired-end data.")
- (license license:gpl2+)))
-
(define-public r-rcas
(package
(name "r-rcas")
--
2.30.1
Ricardo Wurmus <rekado <at> elephly.net>:zimoun <zimon.toutoune <at> gmail.com>:Message #160 received at 48575-done <at> debbugs.gnu.org (full text, mbox):
From: Ricardo Wurmus <rekado <at> elephly.net> To: 48575-done <at> debbugs.gnu.org Subject: [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor). Date: Mon, 31 May 2021 16:07:55 +0200
Thank you for working on this! I have just applied these patches. -- Ricardo
Debbugs Internal Request <help-debbugs <at> gnu.org>
to internal_control <at> debbugs.gnu.org.
(Tue, 29 Jun 2021 11:24:08 GMT) Full text and rfc822 format available.
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.