Bruno Victal <mirai@HIDDEN>
to control <at> debbugs.gnu.org.
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Subject: [PATCH 11/14] gnu: Add r-setrng.
Date: Sat, 25 Mar 2023 00:18:57 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
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Subject: [PATCH 14/14] gnu: Add r-arrayqualitymetrics.
Date: Sat, 25 Mar 2023 00:19:00 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
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To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 13/14] gnu: Add r-beadarray.
Date: Sat, 25 Mar 2023 00:18:59 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
Full text available.
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To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 09/14] gnu: Add r-arraymvout.
Date: Sat, 25 Mar 2023 00:18:55 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
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Subject: [PATCH 10/14] gnu: Add r-arrayquality.
Date: Sat, 25 Mar 2023 00:18:56 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
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To: <62428 <at> debbugs.gnu.org.>
Subject: [PATCH 12/14] gnu: Add r-beaddatapackr.
Date: Sat, 25 Mar 2023 00:18:58 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
Full text available.
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Subject: [PATCH 08/14] gnu: Add r-parody.
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
Full text available.
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Subject: [PATCH 06/14] gnu: Add r-apcomplex.
Date: Sat, 25 Mar 2023 00:18:52 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
Full text available.
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Subject: [PATCH 07/14] gnu: Add r-mdqc.
Date: Sat, 25 Mar 2023 00:18:53 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
Full text available.
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Subject: [PATCH 02/14] gnu: Add r-repmis.
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
Full text available.
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Subject: [PATCH 05/14] gnu: Add r-org-sc-sgd-db.
Date: Sat, 25 Mar 2023 00:18:51 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
Full text available.
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Subject: [PATCH 03/14] gnu: Add r-hybridmtest.
Date: Sat, 25 Mar 2023 00:18:49 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
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Subject: [PATCH 01/14] gnu: Add r-anota2seq.
Date: Sat, 25 Mar 2023 00:18:47 +0100
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* 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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
Full text available.
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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
guix-patches@HIDDEN:bug#62428; Package guix-patches.
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Mădălin Ionel Patrașcu <madalinionel.patrascu@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#62428; Package guix-patches.
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