* [bug#54620] [PATCH 1/3] Add r-rafalib
@ 2022-03-29 7:00 Hong.Li
2022-03-29 7:03 ` [bug#54620] [PATCH 2/3] Add r-stager Hong.Li
2022-03-29 7:04 ` [bug#54620] [PATCH 3/3] Add r-rnaseqdtu Hong.Li
0 siblings, 2 replies; 4+ messages in thread
From: Hong.Li @ 2022-03-29 7:00 UTC (permalink / raw)
To: 54620; +Cc: rekado@elephly.net
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From 5d7cc7fa04bfe2b63dcaeed90359b81fd7ed0679 Mon Sep 17 00:00:00 2001
From: "Li, Hong" <hong.li@mdc-berlin.de>
Date: Mon, 28 Mar 2022 11:39:39 +0200
Subject: [PATCH 1/3] Add r-rafalib
---
gnu/packages/cran.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 23645faa8a..e595de6c2d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7464,6 +7464,26 @@ files.")
environment within Shiny.")
(license license:expat)))
+(define-public r-rafalib
+ (package
+ (name "r-rafalib")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rafalib" version))
+ (sha256
+ (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"))))
+ (properties `((upstream-name . "rafalib")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-rcolorbrewer))
+ (home-page "https://cran.r-project.org/package=rafalib")
+ (synopsis "Convenience Functions for Routine Data Exploration")
+ (description
+ "This package provides a series of shortcuts for routine tasks originally
+developed by Rafael A. Irizarry to facilitate data exploration.")
+ (license license:artistic2.0)))
+
(define-public r-randomizr
(package
(name "r-randomizr")
--
2.26.1
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#54620] [PATCH 2/3] Add r-stager
2022-03-29 7:00 [bug#54620] [PATCH 1/3] Add r-rafalib Hong.Li
@ 2022-03-29 7:03 ` Hong.Li
2022-03-29 7:04 ` [bug#54620] [PATCH 3/3] Add r-rnaseqdtu Hong.Li
1 sibling, 0 replies; 4+ messages in thread
From: Hong.Li @ 2022-03-29 7:03 UTC (permalink / raw)
To: 54620@debbugs.gnu.org; +Cc: rekado@elephly.net
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From 5c0016a8e9b905e6eeae1d682b9db16379030e94 Mon Sep 17 00:00:00 2001
From: "Li, Hong" <hong.li@mdc-berlin.de>
Date: Mon, 28 Mar 2022 11:41:51 +0200
Subject: [PATCH 2/3] Add r-stager
---
gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 55d397e5cf..c22199528e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4739,6 +4739,29 @@ events and allows for the incorporation of prior knowledge through supervised
graph construction.")
(license license:artistic2.0)))
+(define-public r-stager
+ (package
+ (name "r-stager")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "stageR" version))
+ (sha256
+ (base32 "0vpx0v04hgkhzi0bm7ipnb9xr37n5wvnnr45lljgni8pwabfkf6y"))))
+ (properties `((upstream-name . "stageR")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/stageR")
+ (synopsis
+ "stageR: stage-wise analysis of high throughput gene expression data")
+ (description
+ "The stageR package allows automated stage-wise analysis of high-throughput gene
+expression data. The method is published in Genome Biology at
+https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0")
+ (license license:#f)))
+
(define-public r-stringdb
(package
(name "r-stringdb")
--
2.26.1
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#54620] [PATCH 3/3] Add r-rnaseqdtu
2022-03-29 7:00 [bug#54620] [PATCH 1/3] Add r-rafalib Hong.Li
2022-03-29 7:03 ` [bug#54620] [PATCH 2/3] Add r-stager Hong.Li
@ 2022-03-29 7:04 ` Hong.Li
2022-04-06 10:10 ` bug#54620: " Ricardo Wurmus
1 sibling, 1 reply; 4+ messages in thread
From: Hong.Li @ 2022-03-29 7:04 UTC (permalink / raw)
To: 54620@debbugs.gnu.org; +Cc: rekado@elephly.net
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From fdd03ffe8b0db96f4ba662c0367a012267659a30 Mon Sep 17 00:00:00 2001
From: "Li, Hong" <hong.li@mdc-berlin.de>
Date: Mon, 28 Mar 2022 11:44:35 +0200
Subject: [PATCH 3/3] Add r-rnaseqdtu
---
gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ada5965e5f..c79d4ad82d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9009,6 +9009,43 @@ for analyzing gene-level association tests in meta-analyses for binary
trait.")
(license license:gpl3)))
+(define-public r-rnaseqdtu
+ (let ((commit "5bee1e769d2e1dc6a3f1cecb78078050eeb5b9ac") (revision "1"))
+ (package
+ (name "r-rnaseqdtu")
+ (version (git-version "2.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mikelove/rnaseqDTU/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0jfi1ydsk8m5nadwnih48v87nnxdc7s3f0pny4axmnj40dd42as0"))))
+ (properties `((upstream-name . "rnaseqDTU")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-deseq2
+ r-devtools
+ r-dexseq
+ r-drimseq
+ r-edger
+ r-rafalib
+ r-stager))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/mikelove/rnaseqDTU/")
+ (synopsis
+ "RNA-seq workflow for differential transcript usage following Salmon quantification")
+ (description
+ "RNA-seq workflow for differential transcript usage (DTU) following Salmon
+quantification. This workflow uses Bioconductor packages tximport, DRIMSeq, and
+DEXSeq to perform a DTU analysis on simulated data. It also shows how to use
+stageR to perform two-stage testing of DTU, a statistical framework to screen at
+the gene level and then confirm which transcripts within the significant genes
+show evidence of DTU.")
+ (license license:artistic2.0))))
+
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
--
2.26.1
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#54620: [PATCH 3/3] Add r-rnaseqdtu
2022-03-29 7:04 ` [bug#54620] [PATCH 3/3] Add r-rnaseqdtu Hong.Li
@ 2022-04-06 10:10 ` Ricardo Wurmus
0 siblings, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2022-04-06 10:10 UTC (permalink / raw)
To: Hong.Li@mdc-berlin.de; +Cc: 54620-done
Thanks for the patches! I modified them to fix licenses, descriptions,
synopses, indentation, etc, and just pushed them to the “master” branch.
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2022-04-06 10:12 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed)
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2022-03-29 7:00 [bug#54620] [PATCH 1/3] Add r-rafalib Hong.Li
2022-03-29 7:03 ` [bug#54620] [PATCH 2/3] Add r-stager Hong.Li
2022-03-29 7:04 ` [bug#54620] [PATCH 3/3] Add r-rnaseqdtu Hong.Li
2022-04-06 10:10 ` bug#54620: " Ricardo Wurmus
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