* [PATCH 01/25] gnu: Add r-hwriter.
@ 2016-09-21 20:45 Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 02/25] gnu: Add r-rjson Ricardo Wurmus
` (24 more replies)
0 siblings, 25 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/web.scm (r-hwriter): New variable.
---
gnu/packages/web.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 2c63e75..3713b24 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3301,6 +3301,25 @@ where data can be processed either in memory, on disk, or streaming via the
callback or connection interfaces.")
(license l:expat)))
+(define-public r-hwriter
+ (package
+ (name "r-hwriter")
+ (version "1.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "hwriter" version))
+ (sha256
+ (base32
+ "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/hwriter")
+ (synopsis "Output R objects in HTML format")
+ (description
+ "This package provides easy-to-use and versatile functions to output R
+objects in HTML format.")
+ (license l:lgpl2.1+)))
+
(define-public gumbo-parser
(package
(name "gumbo-parser")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 02/25] gnu: Add r-rjson.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 03/25] gnu: Add r-rpart Ricardo Wurmus
` (23 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/web.scm (r-rjson): New variable.
---
gnu/packages/web.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 3713b24..e588014 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3320,6 +3320,25 @@ callback or connection interfaces.")
objects in HTML format.")
(license l:lgpl2.1+)))
+(define-public r-rjson
+ (package
+ (name "r-rjson")
+ (version "0.2.15")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rjson" version))
+ (sha256
+ (base32
+ "1vzjyvf57k1fjizlk28rby65y5lsww5qnfvgnhln74qwda7hvl3p"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/rjson")
+ (synopsis "JSON library for R")
+ (description
+ "This package provides functions to convert R objects into JSON objects
+and vice-versa.")
+ (license l:gpl2+)))
+
(define-public gumbo-parser
(package
(name "gumbo-parser")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 03/25] gnu: Add r-rpart.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 02/25] gnu: Add r-rjson Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 04/25] gnu: Add r-annotate Ricardo Wurmus
` (22 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-rpart): 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 2a9a31e..806aacb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2958,6 +2958,25 @@ noncentral hypergeometric distribution (also called extended hypergeometric
distribution).")
(license license:gpl3+)))
+(define-public r-rpart
+ (package
+ (name "r-rpart")
+ (version "4.1-10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rpart" version))
+ (sha256
+ (base32
+ "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/rpart")
+ (synopsis "Recursive partitioning and regression trees")
+ (description
+ "This package provides recursive partitioning functions for
+classification, regression and survival trees.")
+ (license (list license:gpl2+ license:gpl3+))))
+
(define-public r-runit
(package
(name "r-runit")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 04/25] gnu: Add r-annotate.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 02/25] gnu: Add r-rjson Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 03/25] gnu: Add r-rpart Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 05/25] gnu: Add r-geneplotter Ricardo Wurmus
` (21 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-annotate): 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 7a27e0b..604d781 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5041,6 +5041,32 @@ dissimilarity analysis. Most of its multivariate tools can be used for other
data types as well.")
(license license:gpl2+)))
+(define-public r-annotate
+ (package
+ (name "r-annotate")
+ (version "1.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "annotate" version))
+ (sha256
+ (base32
+ "00wnhbjp5i6a5vyvlq4f5hs8qngjxz7fm869kla1spmd0dp2ynsy"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dbi" ,r-dbi)
+ ("r-xml" ,r-xml)
+ ("r-xtable" ,r-xtable)))
+ (home-page
+ "http://bioconductor.org/packages/annotate")
+ (synopsis "Annotation for microarrays")
+ (description "This package provides R enviroments for the annotation of
+microarrays.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 05/25] gnu: Add r-geneplotter.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (2 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 04/25] gnu: Add r-annotate Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 06/25] gnu: Add r-hmisc Ricardo Wurmus
` (20 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
---
gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 604d781..30f1f6a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5067,6 +5067,31 @@ data types as well.")
microarrays.")
(license license:artistic2.0)))
+(define-public r-geneplotter
+ (package
+ (name "r-geneplotter")
+ (version "1.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "geneplotter" version))
+ (sha256
+ (base32
+ "0lvrywl0251g4y0h0qlgkbg4l83ja5544c85z1wj30qxiy77iqc2"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-lattice" ,r-lattice)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "http://bioconductor.org/packages/geneplotter")
+ (synopsis "Graphics functions for genomic data")
+ (description
+ "This package provides functions for plotting genomic data.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 06/25] gnu: Add r-hmisc.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (3 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 05/25] gnu: Add r-geneplotter Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 07/25] gnu: Add r-genefilter Ricardo Wurmus
` (19 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-hmisc): New variable.
---
gnu/packages/statistics.scm | 39 +++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 806aacb..4a8c64b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -41,6 +41,7 @@
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
#:use-module (gnu packages java)
+ #:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages pcre)
@@ -2977,6 +2978,44 @@ distribution).")
classification, regression and survival trees.")
(license (list license:gpl2+ license:gpl3+))))
+(define-public r-hmisc
+ (package
+ (name "r-hmisc")
+ (version "3.17-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Hmisc" version))
+ (sha256
+ (base32
+ "1hr2kycpm0h3li9gnlbx9pl6h13das7g2wqfk6cip1kx6lv00ypw"))))
+ (properties `((upstream-name . "Hmisc")))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (propagated-inputs
+ `(("r-acepack" ,r-acepack)
+ ("r-cluster" ,r-cluster)
+ ("r-data-table" ,r-data-table)
+ ("r-foreign" ,r-foreign)
+ ("r-formula" ,r-formula)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gtable" ,r-gtable)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-nnet" ,r-nnet)
+ ("r-rpart" ,r-rpart)))
+ (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
+ (synopsis "Miscellaneous data analysis and graphics functions")
+ (description
+ "This package contains many functions useful for data analysis,
+high-level graphics, utility operations, functions for computing sample size
+and power, importing and annotating datasets, imputing missing values,
+advanced table making, variable clustering, character string manipulation,
+conversion of R objects to LaTeX code, and recoding variables.")
+ (license license:gpl2+)))
+
(define-public r-runit
(package
(name "r-runit")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 07/25] gnu: Add r-genefilter.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (4 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 06/25] gnu: Add r-hmisc Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 08/25] gnu: Add r-deseq2 Ricardo Wurmus
` (18 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-genefilter): 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 30f1f6a..18e688f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5092,6 +5092,32 @@ microarrays.")
"This package provides functions for plotting genomic data.")
(license license:artistic2.0)))
+(define-public r-genefilter
+ (package
+ (name "r-genefilter")
+ (version "1.54.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genefilter" version))
+ (sha256
+ (base32
+ "1hmz6as0njvrsrdbgmk72jyclnnqvfdvp6kqv456h43ldq2ajfv5"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "http://bioconductor.org/packages/genefilter")
+ (synopsis "Filter genes from high-throughput experiments")
+ (description
+ "This package provides basic functions for filtering genes from
+high-throughput sequencing experiments.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 08/25] gnu: Add r-deseq2.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (5 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 07/25] gnu: Add r-genefilter Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 09/25] gnu: Add r-matrix Ricardo Wurmus
` (17 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 18e688f..2df63ee 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5118,6 +5118,51 @@ microarrays.")
high-throughput sequencing experiments.")
(license license:artistic2.0)))
+(define-public r-deseq2
+ (package
+ (name "r-deseq2")
+ (version "1.12.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DESeq2" version))
+ (sha256
+ (base32
+ "12h77f0dpi5xaj7aqf50kkyn6lq9j7bcsly1r0ffmyfcszrp1sfx"))))
+ (properties `((upstream-name . "DESeq2")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'link-against-armadillo
+ (lambda _
+ (substitute* "src/Makevars"
+ (("PKG_LIBS =" prefix)
+ (string-append prefix "-larmadillo"))))))))
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hmisc" ,r-hmisc)
+ ("r-iranges" ,r-iranges)
+ ("r-locfit" ,r-locfit)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "http://bioconductor.org/packages/DESeq2")
+ (synopsis "Differential gene expression analysis")
+ (description
+ "This package provides functions to estimate variance-mean dependence in
+count data from high-throughput nucleotide sequencing assays and test for
+differential expression based on a model using the negative binomial
+distribution.")
+ (license license:lgpl3+)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 09/25] gnu: Add r-matrix.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (6 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 08/25] gnu: Add r-deseq2 Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 10/25] gnu: Add r-pheatmap Ricardo Wurmus
` (16 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-matrix): New variable.
---
gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4a8c64b..495445a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -381,6 +381,28 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation(\"Rcpp\")' for details on these last two.")
(license license:gpl2+)))
+(define-public r-matrix
+ (package
+ (name "r-matrix")
+ (version "1.2-7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "Matrix" version))
+ (sha256
+ (base32
+ "18x3mdq5cdhbk1lw5cj7vbr41lk8w9p4i5kzh8wslgq6p3d9ac3c"))))
+ (properties `((upstream-name . "Matrix")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lattice" ,r-lattice)))
+ (home-page "http://Matrix.R-forge.R-project.org/")
+ (synopsis "Sparse and dense matrix classes and methods")
+ (description
+ "This package provides classes and methods for dense and sparse matrices
+and operations on them using LAPACK and SuiteSparse.")
+ (license license:gpl2+)))
+
(define-public r-mgcv
(package
(name "r-mgcv")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 10/25] gnu: Add r-pheatmap.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (7 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 09/25] gnu: Add r-matrix Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 11/25] gnu: Add r-sendmailr Ricardo Wurmus
` (15 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-pheatmap): 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 495445a..728f0fd 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -299,6 +299,30 @@ non-estimable cases correctly.")
\"tables\" of grobs.")
(license license:gpl2+)))
+(define-public r-pheatmap
+ (package
+ (name "r-pheatmap")
+ (version "1.0.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pheatmap" version))
+ (sha256
+ (base32
+ "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-gtable" ,r-gtable)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-scales" ,r-scales)))
+ (home-page
+ "http://cran.r-project.org/web/packages/pheatmap")
+ (synopsis "Pretty heatmaps")
+ (description
+ "This package provides an implementation of heatmaps that offers more
+control over dimensions and appearance.")
+ (license license:gpl2+)))
+
(define-public r-labeling
(package
(name "r-labeling")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 11/25] gnu: Add r-sendmailr.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (8 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 10/25] gnu: Add r-pheatmap Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 12/25] gnu: Add r-backports Ricardo Wurmus
` (14 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-sendmailr): New variable.
---
gnu/packages/statistics.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 728f0fd..d05dfce 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -530,6 +530,29 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org")
;; Includes code licensed under bsd-4
(license license:asl2.0)))
+(define-public r-sendmailr
+ (package
+ (name "r-sendmailr")
+ (version "1.2-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sendmailR" version))
+ (sha256
+ (base32
+ "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
+ (properties `((upstream-name . "sendmailR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-base64enc" ,r-base64enc)))
+ (home-page
+ "http://cran.r-project.org/web/packages/sendmailR")
+ (synopsis "Send email using R")
+ (description
+ "This package contains a simple SMTP client which provides a portable
+solution for sending email, including attachments, from within R.")
+ (license license:gpl2+)))
+
(define-public r-stringi
(package
(name "r-stringi")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 12/25] gnu: Add r-backports.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (9 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 11/25] gnu: Add r-sendmailr Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 13/25] gnu: Add r-checkmate Ricardo Wurmus
` (13 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-backports): New variable.
---
gnu/packages/statistics.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d05dfce..c3dadbd 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1610,6 +1610,29 @@ previous R versions and their release dates.")
limited to R.")
(license license:gpl3+)))
+(define-public r-backports
+ (package
+ (name "r-backports")
+ (version "1.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "backports" version))
+ (sha256
+ (base32
+ "0s04mbb7imqc00jl37i081y4yf7qdimk687dyrkvb20nixvjvjyh"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/backports")
+ (synopsis "Reimplementations of functions introduced since R 3.0.0")
+ (description
+ "Provides implementations of functions which have been introduced in R
+since version 3.0.0. The backports are conditionally exported which results
+in R resolving the function names to the version shipped with R (if available)
+and uses the implemented backports as fallback. This way package developers
+can make use of the new functions without worrying about the minimum required
+R version.")
+ (license license:gpl2+)))
+
(define-public r-brew
(package
(name "r-brew")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 13/25] gnu: Add r-checkmate.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (10 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 12/25] gnu: Add r-backports Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 14/25] gnu: Add r-bbmisc Ricardo Wurmus
` (12 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-checkmate): New variable.
---
gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c3dadbd..1e6f3fd 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1633,6 +1633,28 @@ can make use of the new functions without worrying about the minimum required
R version.")
(license license:gpl2+)))
+(define-public r-checkmate
+ (package
+ (name "r-checkmate")
+ (version "1.8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "checkmate" version))
+ (sha256
+ (base32
+ "1nqyi58jl33af82y8kw8iy9xbna2080y1khhy90kf6lim6q74024"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-backports" ,r-backports)))
+ (home-page "https://github.com/mllg/checkmate")
+ (synopsis "Fast and versatile argument checks")
+ (description
+ "This package provides tests and assertions to perform frequent argument
+checks. A substantial part of the package was written in C to minimize any
+worries about execution time overhead.")
+ (license license:bsd-3)))
+
(define-public r-brew
(package
(name "r-brew")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 14/25] gnu: Add r-bbmisc.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (11 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 13/25] gnu: Add r-checkmate Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 15/25] gnu: Add r-fail Ricardo Wurmus
` (11 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-bbmisc): New variable.
---
gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 1e6f3fd..c8ad5a8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1655,6 +1655,28 @@ checks. A substantial part of the package was written in C to minimize any
worries about execution time overhead.")
(license license:bsd-3)))
+(define-public r-bbmisc
+ (package
+ (name "r-bbmisc")
+ (version "1.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "BBmisc" version))
+ (sha256
+ (base32
+ "0cw2mhw7qhdrx91zzd5iwyh7ch9fy4wxga8j63731q6sxr1airjl"))))
+ (properties `((upstream-name . "BBmisc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-checkmate" ,r-checkmate)))
+ (home-page "https://github.com/berndbischl/BBmisc")
+ (synopsis "Miscellaneous functions for R package development")
+ (description
+ "This package provides miscellaneous helper functions for the development
+of R packages.")
+ (license license:bsd-3)))
+
(define-public r-brew
(package
(name "r-brew")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 15/25] gnu: Add r-fail.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (12 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 14/25] gnu: Add r-bbmisc Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 16/25] gnu: Add r-batchjobs Ricardo Wurmus
` (10 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-fail): New variable.
---
gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c8ad5a8..afe3d7e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1677,6 +1677,28 @@ worries about execution time overhead.")
of R packages.")
(license license:bsd-3)))
+(define-public r-fail
+ (package
+ (name "r-fail")
+ (version "1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fail" version))
+ (sha256
+ (base32
+ "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bbmisc" ,r-bbmisc)
+ ("r-checkmate" ,r-checkmate)))
+ (home-page "https://github.com/mllg/fail")
+ (synopsis "File abstraction interface layer (FAIL)")
+ (description
+ "This package provides a more comfortable interface to work with R data
+or source files in a key-value fashion.")
+ (license license:bsd-3)))
+
(define-public r-brew
(package
(name "r-brew")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 16/25] gnu: Add r-batchjobs.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (13 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 15/25] gnu: Add r-fail Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 17/25] gnu: Add r-annotationforge Ricardo Wurmus
` (9 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/statistics.scm (r-batchjobs): New variable.
---
gnu/packages/statistics.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index afe3d7e..9cf79ef 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1699,6 +1699,37 @@ of R packages.")
or source files in a key-value fashion.")
(license license:bsd-3)))
+(define-public r-batchjobs
+ (package
+ (name "r-batchjobs")
+ (version "1.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "BatchJobs" version))
+ (sha256
+ (base32
+ "1kb99024jih5bycc226bl4jyvbbl1sg72q3m2wnlshl7s8p6vva0"))))
+ (properties `((upstream-name . "BatchJobs")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bbmisc" ,r-bbmisc)
+ ("r-brew" ,r-brew)
+ ("r-checkmate" ,r-checkmate)
+ ("r-dbi" ,r-dbi)
+ ("r-digest" ,r-digest)
+ ("r-fail" ,r-fail)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-sendmailr" ,r-sendmailr)
+ ("r-stringr" ,r-stringr)))
+ (home-page "https://github.com/tudo-r/BatchJobs")
+ (synopsis "Batch computing with R")
+ (description
+ "This package provides @code{Map}, @code{Reduce} and @code{Filter}
+variants to generate jobs on batch computing systems like PBS/Torque, LSF,
+SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
+ (license license:bsd-2)))
+
(define-public r-brew
(package
(name "r-brew")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 17/25] gnu: Add r-annotationforge.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (14 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 16/25] gnu: Add r-batchjobs Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 18/25] gnu: Add r-rbgl Ricardo Wurmus
` (8 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
---
gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2df63ee..a5aadd0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5163,6 +5163,35 @@ differential expression based on a model using the negative binomial
distribution.")
(license license:lgpl3+)))
+(define-public r-annotationforge
+ (package
+ (name "r-annotationforge")
+ (version "1.14.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationForge" version))
+ (sha256
+ (base32
+ "1vkdd1qdv5g680ipw4vwjvn52xn66xpg6ngmwyknz77ckxnnpf4q"))))
+ (properties
+ `((upstream-name . "AnnotationForge")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dbi" ,r-dbi)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)))
+ (home-page "http://bioconductor.org/packages/AnnotationForge")
+ (synopsis "Code for building annotation database packages")
+ (description
+ "This package provides code for generating Annotation packages and their
+databases. Packages produced are intended to be used with AnnotationDbi.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 18/25] gnu: Add r-rbgl.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (15 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 17/25] gnu: Add r-annotationforge Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 19/25] gnu: Add r-gseabase Ricardo Wurmus
` (7 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
---
gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a5aadd0..d9acb00 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5192,6 +5192,27 @@ distribution.")
databases. Packages produced are intended to be used with AnnotationDbi.")
(license license:artistic2.0)))
+(define-public r-rbgl
+ (package
+ (name "r-rbgl")
+ (version "1.48.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RBGL" version))
+ (sha256
+ (base32
+ "1k82zcbyfx3p9hc8r0hwq73krbhakjan8fgbfr6w8z2crfkv3zmz"))))
+ (properties `((upstream-name . "RBGL")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-graph" ,r-graph)))
+ (home-page "http://www.bioconductor.org/packages/RBGL")
+ (synopsis "Interface to the Boost graph library")
+ (description
+ "This package provides a fairly extensive and comprehensive interface to
+the graph algorithms contained in the Boost library.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 19/25] gnu: Add r-gseabase.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (16 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 18/25] gnu: Add r-rbgl Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 20/25] gnu: Add r-category Ricardo Wurmus
` (6 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d9acb00..52fa17c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5213,6 +5213,33 @@ databases. Packages produced are intended to be used with AnnotationDbi.")
the graph algorithms contained in the Boost library.")
(license license:artistic2.0)))
+(define-public r-gseabase
+ (package
+ (name "r-gseabase")
+ (version "1.34.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GSEABase" version))
+ (sha256
+ (base32
+ "0l3y7hq3vabildr6djsn50x0kfgihpbqxwvh7rw6k18pv5k4j72c"))))
+ (properties `((upstream-name . "GSEABase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-graph" ,r-graph)
+ ("r-xml" ,r-xml)))
+ (home-page "http://bioconductor.org/packages/GSEABase")
+ (synopsis "Gene set enrichment data structures and methods")
+ (description
+ "This package provides classes and methods to support @dfn{Gene Set
+Enrichment Analysis} (GSEA).")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 20/25] gnu: Add r-category.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (17 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 19/25] gnu: Add r-gseabase Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 21/25] gnu: Add r-gostats Ricardo Wurmus
` (5 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-category): New variable.
---
gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 52fa17c..d99869e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5240,6 +5240,37 @@ the graph algorithms contained in the Boost library.")
Enrichment Analysis} (GSEA).")
(license license:artistic2.0)))
+(define-public r-category
+ (package
+ (name "r-category")
+ (version "2.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Category" version))
+ (sha256
+ (base32
+ "0c8px9ar589f3iqkbk9vfhwj30dpnxj81h8sfq20cl1cbmcx2a04"))))
+ (properties `((upstream-name . "Category")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genefilter" ,r-genefilter)
+ ("r-graph" ,r-graph)
+ ("r-gseabase" ,r-gseabase)
+ ("r-matrix" ,r-matrix)
+ ("r-rbgl" ,r-rbgl)
+ ("r-rsqlite" ,r-rsqlite)))
+ (home-page "http://bioconductor.org/packages/Category")
+ (synopsis "Category analysis")
+ (description
+ "This package provides a collection of tools for performing category
+analysis.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 21/25] gnu: Add r-gostats.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (18 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 20/25] gnu: Add r-category Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 22/25] gnu: Add r-shortread Ricardo Wurmus
` (4 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
---
gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d99869e..1294964 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5271,6 +5271,36 @@ Enrichment Analysis} (GSEA).")
analysis.")
(license license:artistic2.0)))
+(define-public r-gostats
+ (package
+ (name "r-gostats")
+ (version "2.38.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GOstats" version))
+ (sha256
+ (base32
+ "1hhw6vqr8f3g4jzq0v8f2za0r1h117j5s6av87zxs41cv7dq1wb3"))))
+ (properties `((upstream-name . "GOstats")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationforge" ,r-annotationforge)
+ ("r-biobase" ,r-biobase)
+ ("r-category" ,r-category)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-rbgl" ,r-rbgl)))
+ (home-page "http://bioconductor.org/packages/GOstats")
+ (synopsis "Tools for manipulating GO and microarrays")
+ (description
+ "This package provides a set of tools for interacting with GO and
+microarray data. A variety of basic manipulation tools for graphs, hypothesis
+testing and other simple calculations.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 22/25] gnu: Add r-shortread.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (19 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 21/25] gnu: Add r-gostats Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 23/25] gnu: Add r-systempiper Ricardo Wurmus
` (3 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
---
gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1294964..9915247 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5301,6 +5301,48 @@ microarray data. A variety of basic manipulation tools for graphs, hypothesis
testing and other simple calculations.")
(license license:artistic2.0)))
+(define-public r-shortread
+ (package
+ (name "r-shortread")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ShortRead" version))
+ (sha256
+ (base32
+ "0qlxns4bhwfpafx3km2lnivgl2qyp7n4g1ardm6vrinpq8paxbjg"))))
+ (properties `((upstream-name . "ShortRead")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "http://bioconductor.org/packages/ShortRead")
+ (synopsis "FASTQ input and manipulation tools")
+ (description
+ "This package implements sampling, iteration, and input of FASTQ files.
+It includes functions for filtering and trimming reads, and for generating a
+quality assessment report. Data are represented as
+@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
+purposes. The package also contains legacy support for early single-end,
+ungapped alignment formats.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 23/25] gnu: Add r-systempiper.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (20 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 22/25] gnu: Add r-shortread Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 24/25] gnu: Add r-grohmm Ricardo Wurmus
` (2 subsequent siblings)
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9915247..f3843dd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5343,6 +5343,52 @@ purposes. The package also contains legacy support for early single-end,
ungapped alignment formats.")
(license license:artistic2.0)))
+(define-public r-systempiper
+ (package
+ (name "r-systempiper")
+ (version "1.6.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "systemPipeR" version))
+ (sha256
+ (base32
+ "0s2g46a5d5bvx45i3cgmib48wf8hrniyladhm0f7kgcbfx57248m"))))
+ (properties `((upstream-name . "systemPipeR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-batchjobs" ,r-batchjobs)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq2" ,r-deseq2)
+ ("r-edger" ,r-edger)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-go-db" ,r-go-db)
+ ("r-gostats" ,r-gostats)
+ ("r-limma" ,r-limma)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-rjson" ,r-rjson)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-shortread" ,r-shortread)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://github.com/tgirke/systemPipeR")
+ (synopsis "Next generation sequencing workflow and reporting environment")
+ (description
+ "This R package provides tools for building and running automated
+end-to-end analysis workflows for a wide range of @dfn{next generation
+sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
+Important features include a uniform workflow interface across different NGS
+applications, automated report generation, and support for running both R and
+command-line software, such as NGS aligners or peak/variant callers, on local
+computers or compute clusters. Efficient handling of complex sample sets and
+experimental designs is facilitated by a consistently implemented sample
+annotation infrastructure.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 24/25] gnu: Add r-grohmm.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (21 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 23/25] gnu: Add r-systempiper Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 25/25] gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene Ricardo Wurmus
2016-09-24 7:44 ` [PATCH 01/25] gnu: Add r-hwriter Ludovic Courtès
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-grohmm): 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 f3843dd..07a5ff6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5389,6 +5389,32 @@ experimental designs is facilitated by a consistently implemented sample
annotation infrastructure.")
(license license:artistic2.0)))
+(define-public r-grohmm
+ (package
+ (name "r-grohmm")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "groHMM" version))
+ (sha256
+ (base32
+ "1l9mcyzyc548114ysb9r0q7hgzw3yy7gpiahrzkzj6hblc4f1jyp"))))
+ (properties `((upstream-name . "groHMM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/Kraus-Lab/groHMM")
+ (synopsis "GRO-seq analysis pipeline")
+ (description
+ "This package provides a pipeline for the analysis of GRO-seq data.")
+ (license license:gpl3+)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* [PATCH 25/25] gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (22 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 24/25] gnu: Add r-grohmm Ricardo Wurmus
@ 2016-09-21 20:45 ` Ricardo Wurmus
2016-09-24 7:44 ` [PATCH 01/25] gnu: Add r-hwriter Ludovic Courtès
24 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-21 20:45 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene):
New variable.
---
gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 07a5ff6..346d7a8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5415,6 +5415,38 @@ annotation infrastructure.")
"This package provides a pipeline for the analysis of GRO-seq data.")
(license license:gpl3+)))
+(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
+ (package
+ (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
+ (version "3.2.2")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "http://bioconductor.org/packages/"
+ "release/data/annotation/src/contrib"
+ "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
+ (properties
+ `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-genomicfeatures" ,r-genomicfeatures)))
+ (home-page
+ "http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
+ (synopsis "Annotation package for human genome in TxDb format")
+ (description
+ "This package provides an annotation database of Homo sapiens genome
+data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
+track. The database is exposed as a @code{TxDb} object.")
+ (license license:artistic2.0)))
+
(define-public vsearch
(package
(name "vsearch")
--
2.9.3
^ permalink raw reply related [flat|nested] 27+ messages in thread
* Re: [PATCH 01/25] gnu: Add r-hwriter.
2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
` (23 preceding siblings ...)
2016-09-21 20:45 ` [PATCH 25/25] gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene Ricardo Wurmus
@ 2016-09-24 7:44 ` Ludovic Courtès
2016-09-26 1:09 ` Ricardo Wurmus
24 siblings, 1 reply; 27+ messages in thread
From: Ludovic Courtès @ 2016-09-24 7:44 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Hello!
If you don’t get more feedback, not even from ‘guix lint’, then I guess
you can safely push the 25 patches. :-)
At first sight, they all sound fairly straightforward.
Thanks!
Ludo’.
^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: [PATCH 01/25] gnu: Add r-hwriter.
2016-09-24 7:44 ` [PATCH 01/25] gnu: Add r-hwriter Ludovic Courtès
@ 2016-09-26 1:09 ` Ricardo Wurmus
0 siblings, 0 replies; 27+ messages in thread
From: Ricardo Wurmus @ 2016-09-26 1:09 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel
Ludovic Courtès <ludo@gnu.org> writes:
> If you don’t get more feedback, not even from ‘guix lint’, then I guess
> you can safely push the 25 patches. :-)
Okay, will push them soon! “guix lint” didn’t complain and the packages
have all been in use at the MDC for a while now.
~~ Ricardo
^ permalink raw reply [flat|nested] 27+ messages in thread
end of thread, other threads:[~2016-09-26 5:23 UTC | newest]
Thread overview: 27+ messages (download: mbox.gz follow: Atom feed
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2016-09-21 20:45 [PATCH 01/25] gnu: Add r-hwriter Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 02/25] gnu: Add r-rjson Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 03/25] gnu: Add r-rpart Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 04/25] gnu: Add r-annotate Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 05/25] gnu: Add r-geneplotter Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 06/25] gnu: Add r-hmisc Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 07/25] gnu: Add r-genefilter Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 08/25] gnu: Add r-deseq2 Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 09/25] gnu: Add r-matrix Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 10/25] gnu: Add r-pheatmap Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 11/25] gnu: Add r-sendmailr Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 12/25] gnu: Add r-backports Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 13/25] gnu: Add r-checkmate Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 14/25] gnu: Add r-bbmisc Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 15/25] gnu: Add r-fail Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 16/25] gnu: Add r-batchjobs Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 17/25] gnu: Add r-annotationforge Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 18/25] gnu: Add r-rbgl Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 19/25] gnu: Add r-gseabase Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 20/25] gnu: Add r-category Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 21/25] gnu: Add r-gostats Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 22/25] gnu: Add r-shortread Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 23/25] gnu: Add r-systempiper Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 24/25] gnu: Add r-grohmm Ricardo Wurmus
2016-09-21 20:45 ` [PATCH 25/25] gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene Ricardo Wurmus
2016-09-24 7:44 ` [PATCH 01/25] gnu: Add r-hwriter Ludovic Courtès
2016-09-26 1:09 ` Ricardo Wurmus
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