GNU bug report logs -
#53349
[PATCH 0/9] Add 2 bioinformatics R packages
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Reported by: zimoun <zimon.toutoune <at> gmail.com>
Date: Tue, 18 Jan 2022 17:53:02 UTC
Severity: normal
Tags: patch
Done: Ricardo Wurmus <rekado <at> elephly.net>
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:
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
Hi,
This series adds two bioinformatics R packages and the missing dependencies.
zimoun (9):
gnu: r-org-dr-eg-db: Update to 3.14.0.
gnu: Add r-jetset.
gnu: Add r-hgu133plus2-db.
gnu: Add r-chorddiag.
gnu: Add r-scico.
gnu: Add r-add2ggplot.
gnu: Add r-rlist.
gnu: Add r-icellnet.
gnu: Add r-scseqcomm.
gnu/packages/bioconductor.scm | 53 ++++++++++++++++--
gnu/packages/bioinformatics.scm | 96 ++++++++++++++++++++++++++++++++-
gnu/packages/cran.scm | 69 +++++++++++++++++++++++-
gnu/packages/statistics.scm | 30 +++++++++++
4 files changed, 243 insertions(+), 5 deletions(-)
base-commit: 5ed33b0d05902de921e972d41168910107c93515
--
2.34.0
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Message #8 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/bioconductor.scm (r-org-dr-eg-db): Update to 3.14.0.
---
gnu/packages/bioconductor.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0fbe0965c2..7194e8b0e7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5,7 +5,7 @@
;;; Copyright © 2016 Ben Woodcroft <donttrustben <at> gmail.com>
;;; Copyright © 2017 Efraim Flashner <efraim <at> flashner.co.il>
;;; 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 © 2019, 2020, 2021, 2022 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>
;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
@@ -626,13 +626,13 @@ (define-public r-org-dr-eg-db
(define-public r-org-hs-eg-db
(package
(name "r-org-hs-eg-db")
- (version "3.7.0")
+ (version "3.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
(sha256
(base32
- "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
+ "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j"))))
(properties
`((upstream-name . "org.Hs.eg.db")))
(build-system r-build-system)
--
2.34.0
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Message #11 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/bioconductor.scm (r-hgu133plus2-db): New variable.
---
gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 935c958cd0..aece88ab5b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -956,6 +956,26 @@ (define-public r-do-db
Disease Ontology.")
(license license:artistic2.0)))
+(define-public r-hgu133plus2-db
+ (package
+ (name "r-hgu133plus2-db")
+ (version "3.13.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
+ (sha256
+ (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
+ (properties `((upstream-name . "hgu133plus2.db")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
+ (home-page "https://bioconductor.org/packages/hgu133plus2.db")
+ (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
+ (description
+ "This package provides Affymetrix HG-U133_Plus_2 array annotation
+data (chip hgu133plus2) assembled using data from public repositories.")
+ (license license:artistic2.0)))
+
(define-public r-pfam-db
(package
(name "r-pfam-db")
--
2.34.0
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Message #14 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/statistics.scm (r-chorddiag): New variable.
---
gnu/packages/statistics.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f777ddf332..7fc1de6cc5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -16,6 +16,7 @@
;;; Copyright © 2021 Bonface Munyoki Kilyungi <me <at> bonfacemunyoki.com>
;;; Copyright © 2021 Lars-Dominik Braun <lars <at> 6xq.net>
;;; Copyright © 2021 Frank Pursel <frank.pursel <at> gmail.com>
+;;; Copyright © 2022 Simon Tournier <zimon.toutoune <at> gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -847,6 +848,35 @@ (define-public r-bit64
caching.")
(license license:gpl2)))
+(define-public r-chorddiag
+ (package
+ (name "r-chorddiag")
+ (version "0.1.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mattflor/chorddiag")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1bpy9q861l1hyyiqbx2f7qzp7j7im8bkcfdwgxzk5fm0250p359a"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-htmlwidgets r-rcolorbrewer))
+ (native-inputs
+ (list r-knitr))
+ (home-page "https://github.com/mattflor/chorddiag")
+ (synopsis "Create D3 chord diagram")
+ (description
+ "This package provides tools to create interactive chords diagrams via
+the D3 Javascript library. Chord diagrams show directed relationships among a
+group of entities. This package is based on
+@url{http://bl.ocks.org/mbostock/4062006} with some modifications (fading) and
+additions (tooltips, bipartite diagram type).")
+ (license license:gpl3+)))
+
(define-public r-dichromat
(package
(name "r-dichromat")
--
2.34.0
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Message #17 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/bioconductor.scm (r-jetset): New variable.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7194e8b0e7..935c958cd0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1965,6 +1965,33 @@ (define-public r-deconstructsigs
closely reconstructs the mutational profile.")
(license license:gpl2+)))
+;; This is a CRAN package, but it depends on Bioconductor packages.
+(define-public r-jetset
+ (package
+ (name "r-jetset")
+ (version "3.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "jetset" version))
+ (sha256
+ (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
+ (properties `((upstream-name . "jetset")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
+ (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
+ (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
+ (description
+ "This package provides a one-to-one mapping from gene to \"best\" probe
+set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
+hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
+gene may be measured by multiple probe sets. This can present a mild
+conundrum when attempting to evaluate a gene \"signature\" that is defined by
+gene names rather than by specific probe sets. This package also includes the
+pre-calculated probe set quality scores that were used to define the
+mapping.")
+ (license license:artistic2.0)))
+
;; This is a CRAN package, but it depends on Bioconductor packages.
(define-public r-nmf
(package
--
2.34.0
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Message #20 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/cran.scm (r-add2ggplot): New variable.
---
gnu/packages/cran.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2caa12031b..350ece7d35 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -26910,6 +26910,27 @@ (define-public r-adaptivesparsity
geometric models.")
(license license:lgpl3+)))
+(define-public r-add2ggplot
+ (package
+ (name "r-add2ggplot")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "add2ggplot" version))
+ (sha256
+ (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
+ (properties `((upstream-name . "add2ggplot")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/JiaxiangBU/add2ggplot")
+ (synopsis "Extension for ggplot2")
+ (description "This packages provides tools to create themes and color
+palettes for the package ggplot2.")
+ (license license:expat)))
+
(define-public r-diffusionmap
(package
(name "r-diffusionmap")
--
2.34.0
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Message #23 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/cran.scm (r-scico): New variable.
---
gnu/packages/cran.scm | 26 +++++++++++++++++++++++++-
1 file changed, 25 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ce7655e6a6..2caa12031b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -31,7 +31,7 @@
;;; Copyright © 2020 Antoine Côté <antoine.cote <at> posteo.net>
;;; Copyright © 2020 Arun Isaac <arunisaac <at> systemreboot.net>
;;; Copyright © 2020 Magali Lemes <magalilemes00 <at> gmail.com>
-;;; Copyright © 2020, 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
+;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune <at> gmail.com>
;;; Copyright © 2020 Aniket Patil <aniket112.patil <at> gmail.com>
;;; Copyright © 2021 Marcel Schilling <marcel.schilling <at> uni-luebeck.de>
;;; Copyright © 2021 Guillaume Le Vaillant <glv <at> posteo.net>
@@ -27108,6 +27108,30 @@ (define-public r-warp
observations.")
(license license:expat)))
+(define-public r-scico
+ (package
+ (name "r-scico")
+ (version "1.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "scico" version))
+ (sha256
+ (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3"))))
+ (properties `((upstream-name . "scico")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-scales))
+ (home-page "https://github.com/thomasp85/scico")
+ (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
+ (description
+ "This package provides colour choice in information visualisation. It
+important in order to avoid being mislead by inherent bias in the used colour
+palette. This package provides access to the perceptually uniform and
+colour-blindness friendly palettes developed by Fabio Crameri and released
+under the \"Scientific Colour-Maps\" moniker. The package contains 24
+different palettes and includes both diverging and sequential types.")
+ (license license:expat)))
+
(define-public r-slider
(package
(name "r-slider")
--
2.34.0
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Message #26 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/cran.scm (r-rlist): New variable.
---
gnu/packages/cran.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 350ece7d35..cb64c93f3e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -27178,6 +27178,28 @@ (define-public r-slider
sliding windows are to be created.")
(license license:expat)))
+(define-public r-rlist
+ (package
+ (name "r-rlist")
+ (version "0.4.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rlist" version))
+ (sha256
+ (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
+ (properties `((upstream-name . "rlist")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
+ (home-page "https://renkun-ken.github.io/rlist/")
+ (synopsis "A Toolbox for Non-Tabular Data Manipulation")
+ (description
+ "This package provides a set of functions for data manipulation with
+list objects, including mapping, filtering, grouping, sorting, updating,
+searching, and other useful functions. Most functions are designed to be
+pipeline friendly so that data processing with lists can be chained.")
+ (license license:expat)))
+
(define-public r-rsample
(package
(name "r-rsample")
--
2.34.0
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Message #29 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
---
gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b2bd7fbbc0..6e7974e2d7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7893,6 +7893,56 @@ (define-public r-misha
analyze genomic data resulting from various experiments.")
(license license:gpl2)))
+(define-public r-scseqcomm
+ (let ((commit "01076e703999f1a5aa76419d821b50aebe2b777a")
+ (revision "0"))
+ (package
+ (name "r-scseqcomm")
+ (version (git-version "0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/sysbiobig/scseqcomm")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1fw5si47d6agnz5fibmp2b1sv08pbpwv1j71w57xbav9044i032q"))
+ ;; Delete bundled dependency.
+ (modules '((guix build utils)))
+ (snippet
+ '(delete-file-recursively "other_deps"))))
+ (build-system r-build-system)
+ (inputs
+ (list r-add2ggplot
+ r-chorddiag
+ r-doparallel
+ r-dplyr
+ r-foreach
+ ;;r-grid ;; listed in DESCRIPTION
+ r-gridextra
+ r-ggplot2
+ r-gtable
+ r-htmlwidgets
+ r-igraph
+ r-matrix
+ ;;r-methods ;; listed in DESCRIPTION
+ r-org-hs-eg-db
+ r-psych
+ r-rcolorbrewer
+ r-rlang
+ r-scico
+ r-tidygraph
+ r-topgo))
+ (native-inputs
+ (list r-knitr))
+ (home-page "https://gitlab.com/sysbiobig/scseqcomm")
+ (synopsis "Inter- and intra- cellular signaling from single cell RNA-seq")
+ (description "This package is tools for analysing intercellular and
+intracellular signaling from single cell RNA-seq (scRNA-seq) data.")
+ (license license:gpl3))))
+
(define-public r-shaman
(let ((commit "d6944e8ac7bd1dbd5c6cec646eafc1d19d0ca96f")
(release "2.0")
--
2.34.0
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Message #32 received at 53349 <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
---
gnu/packages/bioinformatics.scm | 46 ++++++++++++++++++++++++++++++++-
1 file changed, 45 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6caeec80f7..b2bd7fbbc0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,7 +21,7 @@
;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki <at> gmail.com>
;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
-;;; Copyright © 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
+;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune <at> gmail.com>
;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
;;;
;;; This file is part of GNU Guix.
@@ -7771,6 +7771,50 @@ (define-public r-archr
"This package is designed to streamline scATAC analyses in R.")
(license license:gpl2+))))
+(define-public r-icellnet
+ ;; v1.0 tagged in 2020, last commit contains many fixes.
+ ;; DESCRIPTION says Version: 0.0.0.9000.
+ (let ((commit "b9c05488fb8b5ea69bd560018966eaf4e25f82a")
+ (revision "0"))
+ (package
+ (name "r-icellnet")
+ (version (git-version "1.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/soumelis-lab/ICELLNET")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0cld7d6xqnvd0zpcpg3sx73an6vdc9divzywgnn6zxnqcd987cnw"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-dir
+ (lambda _ (chdir "icellnet"))))))
+ (propagated-inputs
+ (list r-annotationdbi
+ r-data-table
+ r-dplyr
+ r-ggplot2
+ r-hgu133plus2-db
+ r-jetset
+ r-psych
+ r-reshape2
+ r-rlist))
+ (home-page "https://github.com/soumelis-lab/ICELLNET")
+ (synopsis "Transcriptomic-based framework to dissect cell communication")
+ (description "This packages provides a a transcriptomic-based framework
+to dissect cell communication in a global manner. It integrates an original
+expert-curated database of ligand-receptor interactions taking into account
+multiple subunits expression. Based on transcriptomic profiles (gene
+expression), this package allows to compute communication scores between cells
+and provides several visualization modes that can be helpful to dig into
+cell-cell interaction mechanism and extend biological knowledge.")
+ (license license:gpl3))))
+
(define-public r-scde
(package
(name "r-scde")
--
2.34.0
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to
Ricardo Wurmus <rekado <at> elephly.net>
:
You have taken responsibility.
(Fri, 21 Jan 2022 14:56:02 GMT)
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Notification sent
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zimoun <zimon.toutoune <at> gmail.com>
:
bug acknowledged by developer.
(Fri, 21 Jan 2022 14:56:03 GMT)
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Message #37 received at 53349-done <at> debbugs.gnu.org (full text, mbox):
Hi,
thanks for the patches!
> zimoun (9):
> gnu: r-org-dr-eg-db: Update to 3.14.0.
> gnu: Add r-jetset.
> gnu: Add r-hgu133plus2-db.
> gnu: Add r-chorddiag.
This one contains minified JavaScript. It’s only d3.js, so
it wasn’t hard to take the sources and minify it.
> gnu: Add r-scico.
> gnu: Add r-add2ggplot.
> gnu: Add r-rlist.
> gnu: Add r-icellnet.
> gnu: Add r-scseqcomm.
I pushed them all to the master branch
(ce291b193cadbd6926ddf31af2ac6ed8bd607f44).
--
Ricardo
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(Mon, 24 Jan 2022 14:10:03 GMT)
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Message #40 received at 53349-done <at> debbugs.gnu.org (full text, mbox):
Hi Ricardo,
On Fri, 21 Jan 2022 at 15:55, Ricardo Wurmus <rekado <at> elephly.net> wrote:
> > gnu: Add r-chorddiag.
>
> This one contains minified JavaScript. It’s only d3.js, so
> it wasn’t hard to take the sources and minify it.
Ah sorry. Thanks for catching!
> I pushed them all to the master branch
> (ce291b193cadbd6926ddf31af2ac6ed8bd607f44).
Thanks,
simon
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This bug report was last modified 2 years and 56 days ago.
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