* [PATCH] Add r-acsnminer.
@ 2015-12-17 16:02 Ricardo Wurmus
2015-12-19 14:04 ` Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2015-12-17 16:02 UTC (permalink / raw)
To: guix-devel
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From ee0a863d6b070aa341dd0d404115dfb046db4079 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 17 Dec 2015 16:50:03 +0100
Subject: [PATCH 1/3] gnu: Add r-gtable.
* gnu/packages/statistics.scm (r-gtable): New variable.
---
gnu/packages/statistics.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8beb8c8..21e5c60 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1439,3 +1439,22 @@ the header files from the templated Armadillo library.")
;; later, as is the rest of 'Rcpp'.
(license license:gpl2+)))
+(define-public r-gtable
+ (package
+ (name "r-gtable")
+ (version "0.1.2")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "gtable" version))
+ (sha256
+ (base32
+ "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
+ (properties `((upstream-name . "gtable")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/gtable")
+ (synopsis "Arrange grobs in tables")
+ (description
+ "This package provides tools to make it easier to work with tables of
+grobs.")
+ (license license:gpl2+)))
+
--
2.1.0
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From 2b9a8ba7b6cf400b90fc76361a470976715e1c32 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 17 Dec 2015 16:50:47 +0100
Subject: [PATCH 2/3] gnu: Add r-gridextra.
* gnu/packages/statistics.scm (r-gridextra): New variable.
---
gnu/packages/statistics.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 21e5c60..e62924b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1458,3 +1458,27 @@ the header files from the templated Armadillo library.")
grobs.")
(license license:gpl2+)))
+(define-public r-gridextra
+ (package
+ (name "r-gridextra")
+ (version "2.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "gridExtra" version))
+ (sha256
+ (base32
+ "19yyrfd37c5hxlavb9lca9l26wjhc80rlqhgmfj9k3xhbvvpdp17"))))
+ (properties `((upstream-name . "gridExtra")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gtable" ,r-gtable)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ;for building vignettes
+ (home-page "https://github.com/baptiste/gridextra")
+ (synopsis "Miscellaneous functions for \"Grid\" graphics")
+ (description
+ "This package provides a number of user-level functions to work with
+@code{grid} graphics, notably to arrange multiple grid-based plots on a page,
+and draw tables.")
+ (license license:gpl2+)))
+
--
2.1.0
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From c18418c6ff9d136b38547185c5ab395d828483bf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 17 Dec 2015 16:51:28 +0100
Subject: [PATCH 3/3] gnu: Add r-acsnminer.
* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
---
gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9eb8a07..5d93c52 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3298,6 +3298,32 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
(license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
+(define-public r-acsnminer
+ (package
+ (name "r-acsnminer")
+ (version "0.15.11")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "ACSNMineR" version))
+ (sha256
+ (base32
+ "1dl4drhjyazwm9wxlm8yfppwvvj4h6jxwmz8kfw5bxpb3jdnsqvy"))))
+ (properties `((upstream-name . "ACSNMineR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)))
+ (home-page "http://cran.r-project.org/web/packages/ACSNMineR")
+ (synopsis "Gene enrichment analysis")
+ (description
+ "This package provides tools to compute and represent gene set enrichment
+or depletion from your data based on pre-saved maps from the @dfn{Atlas of
+Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
+enrichment can be run with hypergeometric test or Fisher exact test, and can
+use multiple corrections. Visualization of data can be done either by
+barplots or heatmaps.")
+ (license license:gpl2+)))
+
(define-public r-qtl
(package
(name "r-qtl")
--
2.1.0
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] Add r-acsnminer.
2015-12-17 16:02 [PATCH] Add r-acsnminer Ricardo Wurmus
@ 2015-12-19 14:04 ` Ludovic Courtès
2015-12-21 16:20 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Ludovic Courtès @ 2015-12-19 14:04 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From ee0a863d6b070aa341dd0d404115dfb046db4079 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 17 Dec 2015 16:50:03 +0100
> Subject: [PATCH 1/3] gnu: Add r-gtable.
>
> * gnu/packages/statistics.scm (r-gtable): New variable.
OK!
What’s a “grob” BTW? :-)
> From 2b9a8ba7b6cf400b90fc76361a470976715e1c32 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 17 Dec 2015 16:50:47 +0100
> Subject: [PATCH 2/3] gnu: Add r-gridextra.
>
> * gnu/packages/statistics.scm (r-gridextra): New variable.
OK.
> From c18418c6ff9d136b38547185c5ab395d828483bf Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 17 Dec 2015 16:51:28 +0100
> Subject: [PATCH 3/3] gnu: Add r-acsnminer.
>
> * gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
OK.
Thanks!
Ludo’.
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] Add r-acsnminer.
2015-12-19 14:04 ` Ludovic Courtès
@ 2015-12-21 16:20 ` Ricardo Wurmus
0 siblings, 0 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2015-12-21 16:20 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel
Ludovic Courtès <ludo@gnu.org> writes:
> What’s a “grob” BTW? :-)
I think it stands for “graphical object” or similar, which is used for
plotting. (Lilypond also uses this term for anything that needs to be
arranged in a layout, such as text, note heads, etc).
~~ Ricardo
^ permalink raw reply [flat|nested] 3+ messages in thread
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2015-12-17 16:02 [PATCH] Add r-acsnminer Ricardo Wurmus
2015-12-19 14:04 ` Ludovic Courtès
2015-12-21 16:20 ` Ricardo Wurmus
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