GNU bug report logs - #62428
gnu: Add r-anota2seq, r-hybridmtest, r-apalyzer, r-org-sc-sgd-db, r-apcomplex, r-mdqc, , r-parody, r-arraymvout, r-arrayquality, r-beaddatapackr, r-beadarray, r-arrayqualitymetrics, r-repmis, r-setrng..

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: gnu: Add r-anota2seq, r-hybridmtest, r-apalyzer, r-org-sc-sgd-db,
 r-apcomplex, r-mdqc, , r-parody, r-arraymvout, r-arrayquality, r-beaddatapackr,
 r-beadarray, r-arrayqualitymetrics, r-repmis, r-setrng..
Date: Fri, 24 Mar 2023 23:25:59 +0100

* gnu/packages/bioconductor.scm (r-anota2seq, r-hybridmtest, r-apalyzer, 
r-org-sc-sgd-db, r-apcomplex, r-mdqc,
r-parody, r-arraymvout, r-arrayquality, r-beaddatapackr, r-beadarray, 
r-arrayqualitymetrics): New variables.

* gnu/packages/cran.scm (r-repmis, r-setrng): New variables.

-- 
System Administrator
Bioinformatics and Omics Data Science
BIMSB - MDC

Message #8 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Date: Sat, 25 Mar 2023 00:18:50 +0100

Date: Fri, 24 Mar 2023 00:51:48 +0100
Subject: [PATCH 04/14] gnu: Add r-apalyzer.

* gnu/packages/bioconductor.scm (r-apalyzer): New variable.
---
 gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c58613bea3..3ae0dba919 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9354,6 +9354,51 @@ (define r-rcppnumerical
 @code{Rcpp}.")
    (license license:gpl2+)))
 
+(define-public r-apalyzer
+  (package
+    (name "r-apalyzer")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "APAlyzer" version))
+       (sha256
+        (base32 "1iaz9ircfh5x3z5pibn5vnd4lbbr7m5ypk97xnizn22z41aqrxn3"))))
+    (properties `((upstream-name . "APAlyzer")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-before 'install 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list r-deseq2
+           r-dplyr
+           r-genomicalignments
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-ggrepel
+           r-hybridmtest
+           r-repmis
+           r-rsamtools
+           r-rsubread
+           r-rtracklayer
+           r-summarizedexperiment
+           r-tidyr
+           r-variantannotation))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/RJWANGbioinfo/APAlyzer/")
+    (synopsis "Toolkit for APA analysis using RNA-seq data")
+    (description
+     "The APAlyzer package performs @acronym{3'UTR, Three Prime Untranslated
+Region} @acronym{APA, Alternative polyadenylation}, Intronic APA and gene
+expression analysis using RNA-seq data.")
+    (license license:lgpl3)))
+
 (define-public r-apeglm
   (package
    (name "r-apeglm")
-- 
2.39.2

Message #11 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 01/14] gnu: Add r-anota2seq.
Date: Sat, 25 Mar 2023 00:18:47 +0100

* gnu/packages/bioconductor.scm (r-anota2seq): New variable.
---
 gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fe446df67a..37b649a7d6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12069,6 +12069,42 @@ (define-public r-anota
 the data set is suitable for such analysis.")
     (license license:gpl3)))
 
+(define-public r-anota2seq
+  (package
+    (name "r-anota2seq")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "anota2seq" version))
+       (sha256
+        (base32 "14ggggfa6mdqcb2hfvann9mb66s7a9nxlnh31zblb3mrrjizg1x3"))))
+    (properties `((upstream-name . "anota2seq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-deseq2
+           r-edger
+           r-limma
+           r-multtest
+           r-qvalue
+           r-rcolorbrewer
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/anota2seq")
+    (synopsis "Transcriptome-wide analysis of translational efficiency")
+    (description
+     "The anota2seq package provides analysis of translational efficiency and
+differential expression analysis for polysome-profiling and ribosome-profiling
+studies (two or more sample classes) quantified by RNA sequencing or
+DNA-microarray.  Polysome-profiling and ribosome-profiling typically generate
+data for two RNA sources, translated mRNA and total mRNA.  Analysis of
+differential expression is used to estimate changes within each RNA source.
+Analysis of translational efficiency aims to identify changes in translation
+efficiency leading to altered protein levels that are independent of total mRNA
+levels or buffering, a mechanism regulating translational efficiency so that
+protein levels remain constant despite fluctuating total mRNA levels.")
+    (license license:gpl3)))
+
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")

base-commit: ef71e3290916583973724316e815cee840c1b6d8
-- 
2.39.2

Message #14 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 03/14] gnu: Add r-hybridmtest.
Date: Sat, 25 Mar 2023 00:18:49 +0100

* gnu/packages/bioconductor.scm (r-hybridmtest): New variable.
---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 37b649a7d6..c58613bea3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16248,6 +16248,36 @@ (define-public r-rsbml
 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
     (license license:artistic2.0)))
 
+(define-public r-hybridmtest
+  (package
+    (name "r-hybridmtest")
+    (version "1.42.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HybridMTest" version))
+       (sha256
+        (base32 "0mv092lq8548l306ghgvh8yka1fnyvs7w1yzfjzcchj8vlsb0qns"))))
+    (properties `((upstream-name . "HybridMTest")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-fdrtool
+           r-mass
+           r-survival))
+    (home-page "https://bioconductor.org/packages/HybridMTest")
+    (synopsis "Hybrid multiple testing")
+    (description
+     "This package performs hybrid multiple testing that incorporates method
+selection and assumption evaluations into the analysis using @acronym{EBP,
+empirical Bayes probability} estimates obtained by Grenander density estimation.
+For instance, for 3-group comparison analysis, Hybrid Multiple testing considers
+EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test
+of normality as weigth.  Instead of just using EBPs from F-test only or using H-
+test only, this methodology combines both types of EBPs through EBPs from Shapiro
+Wilk test of normality.  This methodology uses then the law of total EBPs.")
+    (license license:gpl2+)))
+
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-- 
2.39.2

Message #17 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 05/14] gnu: Add r-org-sc-sgd-db.
Date: Sat, 25 Mar 2023 00:18:51 +0100

* gnu/packages/bioconductor.scm (r-org-sc-sgd-db): New variable.
---
 gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3ae0dba919..21aa3476c0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -116,6 +116,27 @@ (define-public r-org-bt-eg-db
 based on mapping using Entrez Gene identifiers.")
     (license license:artistic2.0)))
 
+(define-public r-org-sc-sgd-db
+  (package
+    (name "r-org-sc-sgd-db")
+    (version "3.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "org.Sc.sgd.db" version
+                              'annotation))
+       (sha256
+       (base32 "03b8m4p865kzhjj8zyhmc0ic0n4jyjdl4h8a8xny10b7xs6l0v9f"))))
+    (properties `((upstream-name . "org.Sc.sgd.db")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi))
+    (home-page "https://bioconductor.org/packages/org.Sc.sgd.db")
+    (synopsis "Genome wide annotation for Yeast")
+    (description
+     "Genome wide annotation for Yeast, primarily based on mapping using ORF
+identifiers from @acronym{SGD, Saccharomyces Genome Database}.")
+    (license license:artistic2.0)))
+
 (define-public r-pd-mapping50k-xba240
   (package
     (name "r-pd-mapping50k-xba240")
-- 
2.39.2

Message #20 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 02/14] gnu: Add r-repmis.
Date: Sat, 25 Mar 2023 00:18:48 +0100

* gnu/packages/cran.scm (r-repmis): New variable.
---
 gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a36c845479..325fec402b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2894,6 +2894,40 @@ (define-public r-selectr
 package is a port of the Python package @code{cssselect}.")
     (license license:bsd-3)))
 
+(define-public r-repmis
+  (package
+    (name "r-repmis")
+    (version "0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "repmis" version))
+       (sha256
+        (base32 "0z5mjbsl24yjbl0aawr35grcal44rf2xbwv1hy7bdkms94ix79b5"))))
+    (properties `((upstream-name . "repmis")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-before 'install 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list r-data-table
+           r-digest
+           r-httr
+           r-plyr
+           r-r-cache))
+    (home-page "http://cran.r-project.org/package=repmis")
+    (synopsis "Miscellaneous tools for reproducible research")
+    (description
+     "This package is a colletion of tools to load R packages and automatically
+generate BibTeX files citing them as well as load and cache plain-text and Excel
+formatted data stored on GitHub, and from other sources.")
+    (license license:gpl3+)))
+
 (define-public r-reprex
   (package
     (name "r-reprex")
-- 
2.39.2

Message #23 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 07/14] gnu: Add r-mdqc.
Date: Sat, 25 Mar 2023 00:18:53 +0100

* gnu/packages/bioconductor.scm (r-mdqc): New variable.
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 71d65d64a5..39367dd927 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6968,6 +6968,31 @@ (define-public r-maser
 and visualizaton of alternative splicing events generated by rMATS.")
     (license license:expat)))
 
+(define-public r-mdqc
+  (package
+    (name "r-mdqc")
+    (version "1.60.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mdqc" version))
+       (sha256
+        (base32 "1hn6m0z8q3jnzb0h8m29khgm0cx81cfs3s1j6hlg4wsrwkha1i3w"))))
+    (properties `((upstream-name . "mdqc")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cluster
+           r-mass))
+    (home-page "https://bioconductor.org/packages/mdqc")
+    (synopsis "Mahalanobis distance quality control for microarrays")
+    (description
+     "MDQC is a multivariate quality assessment method for microarrays based on
+quality control (QC) reports.  The Mahalanobis distance of an array's quality
+attributes is used to measure the similarity of the quality of that array
+against the quality of the other arrays.  Then, arrays with unusually high
+distances can be flagged as potentially low-quality.")
+    (license license:lgpl2.0+)))
+
 (define-public r-metagenomeseq
   (package
     (name "r-metagenomeseq")
-- 
2.39.2

Message #26 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 06/14] gnu: Add r-apcomplex.
Date: Sat, 25 Mar 2023 00:18:52 +0100

* gnu/packages/bioconductor.scm (r-apcomplex): New variable.
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 21aa3476c0..71d65d64a5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9420,6 +9420,31 @@ (define-public r-apalyzer
 expression analysis using RNA-seq data.")
     (license license:lgpl3)))
 
+(define-public r-apcomplex
+  (package
+    (name "r-apcomplex")
+    (version "2.64.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "apComplex" version))
+       (sha256
+        (base32 "0ycchrdhx7zh62f0p0gxm7g58m2w3c2lfkaasrwydspd3jx0rsna"))))
+    (properties `((upstream-name . "apComplex")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-graph
+           r-org-sc-sgd-db
+           r-rbgl
+           r-rgraphviz))
+    (home-page "https://bioconductor.org/packages/apComplex")
+    (synopsis "Estimate protein complex membership using AP-MS protein data")
+    (description
+     "This package provides functions to estimate a bipartite graph of protein
+complex membership using @acronym{AP-MS, affinity purification–mass spectrometry}
+data.")
+    (license license:lgpl2.0+)))
+
 (define-public r-apeglm
   (package
    (name "r-apeglm")
-- 
2.39.2

Message #29 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 08/14] gnu: Add r-parody.
Date: Sat, 25 Mar 2023 00:18:54 +0100

* gnu/packages/bioconductor.scm (r-parody): New variable.
---
 gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 39367dd927..9f43c42bee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -18999,6 +18999,27 @@ (define-public r-spp
 other functional sequencing data.")
     (license license:gpl2)))
 
+(define-public r-parody
+  (package
+    (name "r-parody")
+    (version "1.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "parody" version))
+       (sha256
+        (base32 "12i5g4ai7a0p81kvqvz1qw099cy3g71n69pij8w760r3jn0c9ilw"))))
+    (properties `((upstream-name . "parody")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/parody")
+    (synopsis "Parametric and resistant outlier dytection")
+    (description
+     "The parody package provides routines for univariate and multivariate outlier
+detection with a focus on parametric methods, but support for some methods based
+on resistant statistics.")
+    (license license:artistic2.0)))
+
 (define-public r-pathview
   (package
     (name "r-pathview")
-- 
2.39.2

Message #32 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 12/14] gnu: Add r-beaddatapackr.
Date: Sat, 25 Mar 2023 00:18:58 +0100

* gnu/packages/bioconductor.scm (r-beaddatapackr): 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 7a904d3d08..e7ab9c983c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -17963,6 +17963,26 @@ (define-public r-beadarraysnp
 performs copy number calculations and reports.")
     (license license:gpl2)))
 
+(define-public r-beaddatapackr
+  (package
+    (name "r-beaddatapackr")
+    (version "1.50.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BeadDataPackR" version))
+       (sha256
+        (base32 "0309cvc9aq4nb06zysb7jvzd844pvw6jbjiqwhar6fg01cx255j0"))))
+    (properties `((upstream-name . "BeadDataPackR")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/BeadDataPackR")
+    (synopsis "Compression of Illumina BeadArray data")
+    (description
+     "This package provides functionality for the compression and decompression
+of raw bead-level data from the Illumina BeadArray platform.")
+    (license license:gpl2)))
+
 ;; This package includes files that have been taken from kentutils.  Some
 ;; parts of kentutils are not released under a free license, but this package
 ;; only uses files that are also found in the free parts of kentutils.
-- 
2.39.2

Message #35 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 10/14] gnu: Add r-arrayquality.
Date: Sat, 25 Mar 2023 00:18:56 +0100

* gnu/packages/bioconductor.scm (r-arrayquality): New variable.
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 62cd786842..7a904d3d08 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3251,6 +3251,31 @@ (define-public r-arraymvout
 error rate.")
     (license license:artistic2.0)))
 
+(define-public r-arrayquality
+  (package
+    (name "r-arrayquality")
+    (version "1.76.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "arrayQuality" version))
+       (sha256
+        (base32 "0b5q71bpl9ln26622jvchd4f9i4kwayqkm9b75yj0a69imbfcn4s"))))
+    (properties `((upstream-name . "arrayQuality")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-gridbase
+           r-hexbin
+           r-limma
+           r-marray
+           r-rcolorbrewer))
+    (home-page "http://arrays.ucsf.edu/")
+    (synopsis "Assessing array quality on spotted arrays")
+    (description
+     "This package provides functions for performing print-run and array level
+quality assessment.")
+    (license license:lgpl2.0+)))
+
 (define-public r-asafe
   (package
     (name "r-asafe")
-- 
2.39.2

Message #38 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 09/14] gnu: Add r-arraymvout.
Date: Sat, 25 Mar 2023 00:18:55 +0100

* gnu/packages/bioconductor.scm (r-arraymvout): New variable.
---
 gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f43c42bee..62cd786842 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3215,6 +3215,42 @@ (define-public r-arrayexpress
 structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
     (license license:artistic2.0)))
 
+(define-public r-arraymvout
+  (package
+    (name "r-arraymvout")
+    (version "1.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "arrayMvout" version))
+       (sha256
+        (base32 "0g66s64n4qlvhkanp33bbvpi93rsdx5xq0mjr96d0195qbf6k156"))))
+    (properties `((upstream-name . "arrayMvout")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-before 'install 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list r-affy
+           r-affycontam
+           r-biobase
+           r-lumi
+           r-mdqc
+           r-parody))
+    (home-page "https://bioconductor.org/packages/arrayMvout")
+    (synopsis "Multivariate outlier detection for expression array QA")
+    (description
+     "This package supports the application of diverse quality metrics to AffyBatch
+instances, summarizing these metrics via PCA, and then performing parametric
+outlier detection on the PCs to identify aberrant arrays with a fixed Type I
+error rate.")
+    (license license:artistic2.0)))
+
 (define-public r-asafe
   (package
     (name "r-asafe")
-- 
2.39.2

Message #41 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 13/14] gnu: Add r-beadarray.
Date: Sat, 25 Mar 2023 00:18:59 +0100

* gnu/packages/bioconductor.scm (r-beadarray): New variable.
---
 gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e7ab9c983c..6c114efd21 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -17943,6 +17943,40 @@ (define-public r-beachmat
 matrices.")
     (license license:gpl3)))
 
+(define-public r-beadarray
+  (package
+    (name "r-beadarray")
+    (version "2.48.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "beadarray" version))
+       (sha256
+        (base32 "0fr24gj6h2rr1r4l3n8myjaihjqi5yinwdsxqa5ih8m3v72dlrby"))))
+    (properties `((upstream-name . "beadarray")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationdbi
+           r-beaddatapackr
+           r-biobase
+           r-biocgenerics
+           r-genomicranges
+           r-ggplot2
+           r-hexbin
+           r-illuminaio
+           r-iranges
+           r-limma
+           r-reshape2))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/beadarray")
+    (synopsis
+     "Quality assessment and low-level analysis for Illumina BeadArray data")
+    (description
+     "The package is able to read bead-level data (raw TIFFs and text files)
+output by BeadScan as well as bead-summary data from BeadStudio.  Methods for
+quality assessment and low-level analysis are provided.")
+    (license license:expat)))
+
 (define-public r-beadarraysnp
   (package
     (name "r-beadarraysnp")
-- 
2.39.2

Message #44 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 14/14] gnu: Add r-arrayqualitymetrics.
Date: Sat, 25 Mar 2023 00:19:00 +0100

* gnu/packages/bioconductor.scm (r-arrayqualitymetrics): New variable.
---
 gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6c114efd21..8792c94d29 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3190,6 +3190,44 @@ (define-public r-antiprofiles
 tumor samples from healthy controls.")
     (license license:artistic2.0)))
 
+(define-public r-arrayqualitymetrics
+  (package
+    (name "r-arrayqualitymetrics")
+    (version "3.54.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "arrayQualityMetrics" version))
+       (sha256
+        (base32 "0jz9b3f8x1aal4sskq1a09jpavhm8alggwbj3ka42fb89xymrz33"))))
+    (properties `((upstream-name . "arrayQualityMetrics")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affy
+           r-affyplm
+           r-beadarray
+           r-biobase
+           r-genefilter
+           r-gridsvg
+           r-hmisc
+           r-hwriter
+           r-lattice
+           r-latticeextra
+           r-limma
+           r-rcolorbrewer
+           r-setrng
+           r-svglite
+           r-vsn
+           r-xml))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/arrayQualityMetrics")
+    (synopsis "Quality metrics report for microarray data sets")
+    (description
+     "This package generates microarray quality metrics reports for data in
+Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch).
+One and two color array platforms are supported.")
+    (license license:lgpl2.0+)))
+
 (define-public r-arrayexpress
   (package
     (name "r-arrayexpress")
-- 
2.39.2

Message #47 received at 62428 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 11/14] gnu: Add r-setrng.
Date: Sat, 25 Mar 2023 00:18:57 +0100

* gnu/packages/cran.scm (r-setrng): 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 325fec402b..bfcafea355 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20170,6 +20170,28 @@ (define-public r-bedr
 additional utilities for genomic regions processing.")
     (license license:gpl2)))
 
+(define-public r-setrng
+  (package
+    (name "r-setrng")
+    (version "2022.4-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "setRNG" version))
+       (sha256
+        (base32 "09089vr5x8snwxh38kdhgpjl3jl7zrk056f6f9a2jg5lsrmnxh31"))))
+    (properties `((upstream-name . "setRNG")))
+    (build-system r-build-system)
+    (home-page "http://distr.r-forge.r-project.org/")
+    (synopsis "Set (normal) random number generator and seed")
+    (description
+     "This package provides utilities to help set and record the setting of the
+seed and the uniform and normal generators used when a random experiment is run.
+The utilities can be used in other functions that do random experiments to simplify
+recording and/or setting all the necessary information for reproducibility.  See
+the vignette and reference manual for examples.")
+    (license license:gpl2)))
+
 (define-public r-sets
   (package
     (name "r-sets")
-- 
2.39.2

Message #54 received at 62428-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 62428-done <at> debbugs.gnu.org 
Subject: gnu: Add r-anota2seq …
Date: Wed, 04 Oct 2023 11:06:07 +0200

I’ve rebased this, updated all packages, fixed indentation, replaced
gexp syntax with simple quote, and removed duplicates.

Thanks for the patches!  Closing.

-- 
Ricardo

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