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authorMark H Weaver <mhw@netris.org>2017-08-15 03:10:14 -0400
committerMark H Weaver <mhw@netris.org>2017-08-15 03:10:14 -0400
commit09ec5a0f0c40afde63975af9e9203884dad86ea7 (patch)
treec85530d4a7ed433779d787a0c452ed0d4b7f0f0a /gnu/packages/bioinformatics.scm
parent3785e42e5219a86d9d8a5208ff18e97e0cbcbe78 (diff)
parent2d430f29231d0d817459d86e0fe15089372e9547 (diff)
downloadpatches-09ec5a0f0c40afde63975af9e9203884dad86ea7.tar
patches-09ec5a0f0c40afde63975af9e9203884dad86ea7.tar.gz
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm106
1 files changed, 106 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f0c4e7748a..87cf164c1a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5796,6 +5796,49 @@ 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")
@@ -9759,3 +9802,66 @@ 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+)))