* [bug#28029] [PATCH 1/2] gnu: Add r-dexseq.
@ 2017-08-09 17:40 Ricardo Wurmus
2017-08-09 17:40 ` [bug#28030] [PATCH 2/2] gnu: Add bismark Ricardo Wurmus
2017-08-09 18:04 ` [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Roel Janssen
0 siblings, 2 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2017-08-09 17:40 UTC (permalink / raw)
To: 28029; +Cc: Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
---
gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 02b338be6..478a756fb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5791,6 +5791,49 @@ differential expression based on a model using the negative binomial
distribution.")
(license license:lgpl3+)))
+(define-public r-dexseq
+ (package
+ (name "r-dexseq")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEXSeq" version))
+ (sha256
+ (base32
+ "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg"))))
+ (properties `((upstream-name . "DEXSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biomart" ,r-biomart)
+ ("r-deseq2" ,r-deseq2)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-statmod" ,r-statmod)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "http://bioconductor.org/packages/DEXSeq")
+ (synopsis "Inference of differential exon usage in RNA-Seq")
+ (description
+ "This package is focused on finding differential exon usage using RNA-seq
+exon counts between samples with different experimental designs. It provides
+functions that allows the user to make the necessary statistical tests based
+on a model that uses the negative binomial distribution to estimate the
+variance between biological replicates and generalized linear models for
+testing. The package also provides functions for the visualization and
+exploration of the results.")
+ (license license:gpl3+)))
+
(define-public r-annotationforge
(package
(name "r-annotationforge")
--
2.13.0
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [bug#28030] [PATCH 2/2] gnu: Add bismark.
2017-08-09 17:40 [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Ricardo Wurmus
@ 2017-08-09 17:40 ` Ricardo Wurmus
2017-08-16 8:51 ` bug#28030: " Ricardo Wurmus
2017-08-09 18:04 ` [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Roel Janssen
1 sibling, 1 reply; 5+ messages in thread
From: Ricardo Wurmus @ 2017-08-09 17:40 UTC (permalink / raw)
To: 28030; +Cc: Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark): New variable.
---
gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 63 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 478a756fb..debe32961 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9794,3 +9794,66 @@ such as transcription factor binding sites (ChIP-seq) or regions of open
chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
Browser.")
(license license:gpl3+))))
+
+(define-public bismark
+ (package
+ (name "bismark")
+ (version "0.16.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/FelixKrueger/Bismark/"
+ "archive/" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
+ (build-system perl-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin"))
+ (docdir (string-append (assoc-ref outputs "out")
+ "/share/doc/bismark"))
+ (docs '("Bismark_User_Guide.pdf"
+ "RELEASE_NOTES.txt"))
+ (scripts '("bismark"
+ "bismark_genome_preparation"
+ "bismark_methylation_extractor"
+ "bismark2bedGraph"
+ "bismark2report"
+ "coverage2cytosine"
+ "deduplicate_bismark"
+ "bismark_sitrep.tpl"
+ "bam2nuc"
+ "bismark2summary")))
+ (mkdir-p docdir)
+ (mkdir-p bin)
+ (for-each (lambda (file) (install-file file bin))
+ scripts)
+ (for-each (lambda (file) (install-file file docdir))
+ docs)
+ #t))))))
+ (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
+ (synopsis "Map bisulfite treated sequence reads and analyze methylation")
+ (description "Bismark is a program to map bisulfite treated sequencing
+reads to a genome of interest and perform methylation calls in a single step.
+The output can be easily imported into a genome viewer, such as SeqMonk, and
+enables a researcher to analyse the methylation levels of their samples
+straight away. Its main features are:
+
+@itemize
+@item Bisulfite mapping and methylation calling in one single step
+@item Supports single-end and paired-end read alignments
+@item Supports ungapped and gapped alignments
+@item Alignment seed length, number of mismatches etc are adjustable
+@item Output discriminates between cytosine methylation in CpG, CHG
+ and CHH context
+@end itemize\n")
+ (license license:gpl3+)))
--
2.13.0
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [bug#28029] [PATCH 1/2] gnu: Add r-dexseq.
2017-08-09 17:40 [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Ricardo Wurmus
2017-08-09 17:40 ` [bug#28030] [PATCH 2/2] gnu: Add bismark Ricardo Wurmus
@ 2017-08-09 18:04 ` Roel Janssen
2017-08-14 10:03 ` bug#28029: " Ricardo Wurmus
1 sibling, 1 reply; 5+ messages in thread
From: Roel Janssen @ 2017-08-09 18:04 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: 28029
Ricardo Wurmus writes:
> * gnu/packages/bioinformatics.scm (r-dexseq): New variable.
> ---
> gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
> 1 file changed, 43 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 02b338be6..478a756fb 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -5791,6 +5791,49 @@ differential expression based on a model using the negative binomial
> distribution.")
> (license license:lgpl3+)))
>
> +(define-public r-dexseq
> + (package
> + (name "r-dexseq")
> + (version "1.22.0")
> + (source
> + (origin
> + (method url-fetch)
> + (uri (bioconductor-uri "DEXSeq" version))
> + (sha256
> + (base32
> + "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg"))))
> + (properties `((upstream-name . "DEXSeq")))
> + (build-system r-build-system)
> + (propagated-inputs
> + `(("r-annotationdbi" ,r-annotationdbi)
> + ("r-biobase" ,r-biobase)
> + ("r-biocgenerics" ,r-biocgenerics)
> + ("r-biocparallel" ,r-biocparallel)
> + ("r-biomart" ,r-biomart)
> + ("r-deseq2" ,r-deseq2)
> + ("r-genefilter" ,r-genefilter)
> + ("r-geneplotter" ,r-geneplotter)
> + ("r-genomicranges" ,r-genomicranges)
> + ("r-hwriter" ,r-hwriter)
> + ("r-iranges" ,r-iranges)
> + ("r-rcolorbrewer" ,r-rcolorbrewer)
> + ("r-rsamtools" ,r-rsamtools)
> + ("r-s4vectors" ,r-s4vectors)
> + ("r-statmod" ,r-statmod)
> + ("r-stringr" ,r-stringr)
> + ("r-summarizedexperiment" ,r-summarizedexperiment)))
> + (home-page "http://bioconductor.org/packages/DEXSeq")
> + (synopsis "Inference of differential exon usage in RNA-Seq")
> + (description
> + "This package is focused on finding differential exon usage using RNA-seq
> +exon counts between samples with different experimental designs. It provides
> +functions that allows the user to make the necessary statistical tests based
> +on a model that uses the negative binomial distribution to estimate the
> +variance between biological replicates and generalized linear models for
> +testing. The package also provides functions for the visualization and
> +exploration of the results.")
> + (license license:gpl3+)))
> +
> (define-public r-annotationforge
> (package
> (name "r-annotationforge")
I have an almost identical package, so LGTM!
Kind regards,
Roel Janssen
^ permalink raw reply [flat|nested] 5+ messages in thread
* bug#28029: [PATCH 1/2] gnu: Add r-dexseq.
2017-08-09 18:04 ` [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Roel Janssen
@ 2017-08-14 10:03 ` Ricardo Wurmus
0 siblings, 0 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2017-08-14 10:03 UTC (permalink / raw)
To: Roel Janssen; +Cc: 28029-done
Roel Janssen <roel@gnu.org> writes:
> Ricardo Wurmus writes:
>
>> * gnu/packages/bioinformatics.scm (r-dexseq): New variable.
[…]
> I have an almost identical package, so LGTM!
Thanks for verifying the package :) I’ve pushed these two patches to
master.
-- Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread
* bug#28030: [PATCH 2/2] gnu: Add bismark.
2017-08-09 17:40 ` [bug#28030] [PATCH 2/2] gnu: Add bismark Ricardo Wurmus
@ 2017-08-16 8:51 ` Ricardo Wurmus
0 siblings, 0 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2017-08-16 8:51 UTC (permalink / raw)
To: 28030-done
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
> * gnu/packages/bioinformatics.scm (bismark): New variable.
> ---
This has been pushed along with r-dexseq.
-- Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2017-08-16 8:52 UTC | newest]
Thread overview: 5+ messages (download: mbox.gz follow: Atom feed
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2017-08-09 17:40 [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Ricardo Wurmus
2017-08-09 17:40 ` [bug#28030] [PATCH 2/2] gnu: Add bismark Ricardo Wurmus
2017-08-16 8:51 ` bug#28030: " Ricardo Wurmus
2017-08-09 18:04 ` [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Roel Janssen
2017-08-14 10:03 ` bug#28029: " Ricardo Wurmus
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