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-rw-r--r--gnu/packages/bioinformatics.scm195
1 files changed, 192 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87cf164c1a..c5157046ab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -311,6 +311,7 @@ BAM files.")
(sha256
(base32
"0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
+ (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
(modules '((guix build utils)))
(snippet
;; Delete bundled htslib.
@@ -2114,7 +2115,7 @@ identify enrichments with functional annotations of the genome.")
(define-public diamond
(package
(name "diamond")
- (version "0.9.9")
+ (version "0.9.10")
(source (origin
(method url-fetch)
(uri (string-append
@@ -2123,7 +2124,7 @@ identify enrichments with functional annotations of the genome.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "04i03046g3l2vk9722z47r1p7j415g97vvz6d76ywmbawyiihcb1"))))
+ "13qqzwg54n5dqh8pm5n3v8x6gqbczzakphwwjix63qv60hcd5bqd"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
@@ -8315,6 +8316,30 @@ package, and for letting R applications work on datasets that are larger than
the available RAM.")
(license license:artistic2.0)))
+(define-public r-annotationfilter
+ (package
+ (name "r-annotationfilter")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationFilter" version))
+ (sha256
+ (base32
+ "0pxvswjzwibdfmrkdragxmzcl844z73pmkn82z92wahwa6gjfyi7"))))
+ (properties
+ `((upstream-name . "AnnotationFilter")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomicranges" ,r-genomicranges)
+ ("r-lazyeval" ,r-lazyeval)))
+ (home-page "https://github.com/Bioconductor/AnnotationFilter")
+ (synopsis "Facilities for filtering Bioconductor annotation resources")
+ (description
+ "This package provides classes and other infrastructure to implement
+filters for manipulating Bioconductor annotation resources. The filters are
+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
+ (license license:artistic2.0)))
+
(define-public emboss
(package
(name "emboss")
@@ -8672,6 +8697,52 @@ CopywriteR constitutes a widely applicable alternative to available copy
number detection tools.")
(license license:gpl2)))
+(define-public r-methylkit
+ (package
+ (name "r-methylkit")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "methylKit" version))
+ (sha256
+ (base32
+ "02acdjf6jl0c1glymin84pdna4farn4vv0gb6107d9iqz3y3gkmm"))))
+ (properties `((upstream-name . "methylKit")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-emdbook" ,r-emdbook)
+ ("r-fastseg" ,r-fastseg)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-limma" ,r-limma)
+ ("r-mclust" ,r-mclust)
+ ("r-qvalue" ,r-qvalue)
+ ("r-r-utils" ,r-r-utils)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://code.google.com/p/methylkit/")
+ (synopsis
+ "DNA methylation analysis from high-throughput bisulfite sequencing results")
+ (description
+ "MethylKit is an R package for DNA methylation analysis and annotation
+from high-throughput bisulfite sequencing. The package is designed to deal
+with sequencing data from @dfn{Reduced representation bisulfite
+sequencing} (RRBS) and its variants, but also target-capture methods and whole
+genome bisulfite sequencing. It also has functions to analyze base-pair
+resolution 5hmC data from experimental protocols such as oxBS-Seq and
+TAB-Seq.")
+ (license license:artistic2.0)))
+
(define-public r-sva
(package
(name "r-sva")
@@ -8816,7 +8887,8 @@ proteomics packages.")
(properties `((upstream-name . "mzR")))
(build-system r-build-system)
(inputs
- `(("netcdf" ,netcdf)))
+ `(("boost" ,boost)
+ ("netcdf" ,netcdf)))
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
@@ -9234,6 +9306,123 @@ distributional differences between lanes (e.g., sequencing depth):
global-scaling and full-quantile normalization.")
(license license:artistic2.0)))
+(define-public r-interactivedisplaybase
+ (package
+ (name "r-interactivedisplaybase")
+ (version "1.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "interactiveDisplayBase" version))
+ (sha256
+ (base32
+ "12f6ap4bl3h2iwwhg8i3r9a7yyd28d8i5lb3fj1vnfvjs762r7r7"))))
+ (properties
+ `((upstream-name . "interactiveDisplayBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-shiny" ,r-shiny)))
+ (home-page "http://bioconductor.org/packages/interactiveDisplayBase")
+ (synopsis "Base package for web displays of Bioconductor objects")
+ (description
+ "This package contains the basic methods needed to generate interactive
+Shiny-based display methods for Bioconductor objects.")
+ (license license:artistic2.0)))
+
+(define-public r-annotationhub
+ (package
+ (name "r-annotationhub")
+ (version "2.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationHub" version))
+ (sha256
+ (base32
+ "1nh5si3j1nv37jcg4260582ayjg18851np47cskrm54prnvhwd9r"))))
+ (properties `((upstream-name . "AnnotationHub")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocinstaller" ,r-biocinstaller)
+ ("r-httr" ,r-httr)
+ ("r-interactivedisplaybase" ,r-interactivedisplaybase)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-yaml" ,r-yaml)))
+ (home-page "http://bioconductor.org/packages/AnnotationHub")
+ (synopsis "Client to access AnnotationHub resources")
+ (description
+ "This package provides a client for the Bioconductor AnnotationHub web
+resource. The AnnotationHub web resource provides a central location where
+genomic files (e.g. VCF, bed, wig) and other resources from standard
+locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
+metadata about each resource, e.g., a textual description, tags, and date of
+modification. The client creates and manages a local cache of files retrieved
+by the user, helping with quick and reproducible access.")
+ (license license:artistic2.0)))
+
+(define-public r-fastseg
+ (package
+ (name "r-fastseg")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "fastseg" version))
+ (sha256
+ (base32
+ "083wiz03q9mynwchs9frlpp6c84dncri5ncibx6h82p228cpja6h"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
+ (synopsis "Fast segmentation algorithm for genetic sequencing data")
+ (description
+ "Fastseg implements a very fast and efficient segmentation algorithm.
+It can segment data from DNA microarrays and data from next generation
+sequencing for example to detect copy number segments. Further it can segment
+data from RNA microarrays like tiling arrays to identify transcripts. Most
+generally, it can segment data given as a matrix or as a vector. Various data
+formats can be used as input to fastseg like expression set objects for
+microarrays or GRanges for sequencing data.")
+ (license license:lgpl2.0+)))
+
+(define-public r-qvalue
+ (package
+ (name "r-qvalue")
+ (version "2.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "qvalue" version))
+ (sha256
+ (base32
+ "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-reshape2" ,r-reshape2)))
+ (home-page "http://github.com/jdstorey/qvalue")
+ (synopsis "Q-value estimation for false discovery rate control")
+ (description
+ "This package takes a list of p-values resulting from the simultaneous
+testing of many hypotheses and estimates their q-values and local @dfn{false
+discovery rate} (FDR) values. The q-value of a test measures the proportion
+of false positives incurred when that particular test is called significant.
+The local FDR measures the posterior probability the null hypothesis is true
+given the test's p-value. Various plots are automatically generated, allowing
+one to make sensible significance cut-offs. The software can be applied to
+problems in genomics, brain imaging, astrophysics, and data mining.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
(define htslib-for-sambamba
(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
(package