diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 278 |
1 files changed, 200 insertions, 78 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 50b0bfaa03..c930099179 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,11 +1,12 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1098,7 +1099,7 @@ confidence to have in an alignment.") ("pigz" ,pigz) ("zlib" ,zlib))) (supported-systems '("x86_64-linux")) - (home-page "http://sourceforge.net/p/bless-ec/wiki/Home/") + (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") (synopsis "Bloom-filter-based error correction tool for NGS reads") (description "@dfn{Bloom-filter-based error correction solution for high-throughput @@ -1479,15 +1480,15 @@ high-throughput sequencing data – with an emphasis on simplicity.") (define-public cd-hit (package (name "cd-hit") - (version "4.6.5") + (version "4.6.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/weizhongli/cdhit" "/releases/download/V" version - "/cd-hit-v" version "-2016-0304.tar.gz")) + "/cd-hit-v" version "-2016-0711.tar.gz")) (sha256 (base32 - "15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3")))) + "1w8hd4fszgg29nqiz569fldwy012la77nljcmlhglgicws56z54p")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests @@ -1806,7 +1807,7 @@ preparation protocols.") (define-public cutadapt (package (name "cutadapt") - (version "1.8") + (version "1.12") (source (origin (method url-fetch) (uri (string-append @@ -1815,27 +1816,30 @@ preparation protocols.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5")))) + "19smhh6444ikn4jlmyhvffw4m5aw7yg07rqsk7arg8dkwyga1i4v")))) (build-system python-build-system) (arguments - ;; tests must be run after install - `(#:phases (alist-cons-after - 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (setenv "PYTHONPATH" - (string-append - (getenv "PYTHONPATH") - ":" (assoc-ref outputs "out") - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages")) - (zero? (system* "nosetests" "-P" "tests"))) - (alist-delete 'check %standard-phases)))) + `(#:phases + (modify-phases %standard-phases + ;; The tests must be run after installation. + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (setenv "PYTHONPATH" + (string-append + (getenv "PYTHONPATH") + ":" (assoc-ref outputs "out") + "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") 5) 3) + "/site-packages")) + (zero? (system* "nosetests" "-P" "tests"))))))) + (inputs + `(("python-xopen" ,python-xopen))) (native-inputs `(("python-cython" ,python-cython) ("python-nose" ,python-nose))) - (home-page "https://code.google.com/p/cutadapt/") + (home-page "https://cutadapt.readthedocs.io/en/stable/") (synopsis "Remove adapter sequences from nucleotide sequencing reads") (description "Cutadapt finds and removes adapter sequences, primers, poly-A tails and @@ -1929,19 +1933,14 @@ accessing bigWig files.") (define-public python-dendropy (package (name "python-dendropy") - (version "4.1.0") + (version "4.2.0") (source (origin (method url-fetch) (uri (pypi-uri "DendroPy" version)) (sha256 (base32 - "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63")) - ;; There are two known test failures that will be fixed in the next - ;; release after 4.1.0. - ;; https://github.com/jeetsukumaran/DendroPy/issues/48 - (patches (search-patches - "python-dendropy-exclude-failing-tests.patch")))) + "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") @@ -1956,15 +1955,6 @@ trees (phylogenies) and characters.") (let ((base (package-with-python2 (strip-python2-variant python-dendropy)))) (package (inherit base) - ;; Do not use same source as 'python-dendropy' because the patched - ;; failing tests do not occur on Python 2. - (source - (origin - (method url-fetch) - (uri (pypi-uri "DendroPy" (package-version base))) - (sha256 - (base32 - "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63")))) (arguments `(#:python ,python-2 #:phases @@ -2020,7 +2010,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.29") + (version "0.8.31") (source (origin (method url-fetch) (uri (string-append @@ -2029,7 +2019,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1mnhj7y13pk2bhfichjma5aw8ssdiqyria61ip1kps6facqlal3z")))) + "0nh79f4rpgq8vmlga743r7vd0z0ik6spy34f7vfq0v9lcmvfr7xq")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -4252,7 +4242,7 @@ viewer.") `(("perl" ,perl) ("zlib" ,zlib))) (supported-systems '("x86_64-linux")) - (home-page "https://code.google.com/p/mosaik-aligner/") + (home-page "https://github.com/wanpinglee/MOSAIK") (synopsis "Map nucleotide sequence reads to reference genomes") (description "MOSAIK is a program for mapping second and third-generation sequencing @@ -4913,7 +4903,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (define-public star (package (name "star") - (version "2.5.2a") + (version "2.5.2b") (source (origin (method url-fetch) (uri (string-append "https://github.com/alexdobin/STAR/archive/" @@ -4921,7 +4911,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0xjlsm4p9flln111hv4xx7xy94c2nl53zvdvbk9winmiradjsdra")) + "1na6np880r1zaamiy00hy8bid5anpy0kgf63587v2yl080krk2zq")) (modules '((guix build utils))) (snippet '(begin @@ -4930,6 +4920,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") ;; Remove pre-built binaries and bundled htslib sources. (delete-file-recursively "bin/MacOSX_x86_64") (delete-file-recursively "bin/Linux_x86_64") + (delete-file-recursively "bin/Linux_x86_64_static") (delete-file-recursively "source/htslib") #t)))) (build-system gnu-build-system) @@ -5211,20 +5202,21 @@ data types as well.") (define-public r-annotate (package (name "r-annotate") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "1fd2csq7dcs2gwndgwdx2nwkymz8gsmlnqqzv3p0vjjsvvq5n2a8")))) + "0yymz8qxgnbybvfhqrgkd1hh9dhwxdii1yxkhr1zicjgb35xixxb")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) + ("r-rcurl" ,r-rcurl) ("r-xml" ,r-xml) ("r-xtable" ,r-xtable))) (home-page @@ -5288,14 +5280,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0kq06jy4xg5ii3a9l62f17kirsfx0gsiwq6mhiy985cqzpdn893g")))) + "1walwkqryn1gnwz7zryr5764a0p6ia7ag4w6w9n8fskg8dkg0fqs")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (arguments @@ -5805,14 +5797,14 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") (define-public bioruby (package (name "bioruby") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (rubygems-uri "bio" version)) (sha256 (base32 - "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc")))) + "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49")))) (build-system ruby-build-system) (propagated-inputs `(("ruby-libxml" ,ruby-libxml))) @@ -5941,13 +5933,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0qbk23fz8cn260isd9xlh9lxfj4adar6iqzai01c4kz0p31f45za")))) + "0sl99xw940ixrm6v24lgaw3ljh56g59a6rdz7g160hx84z9f8n2n")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -6076,13 +6068,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.12.0") + (version "0.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0m0npc0vhmcwcxws7v2f8k4hvvrjvnlrsr94klxf4a8m4xw2xzzk")))) + "0i36y3w36h3d8rmazxcrip4gvn54rd9av1wz4lygsprrjmylfhcc")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -6128,13 +6120,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0cdl1sfd3cvf93lnz91fdk64fbg1mnd5g958dwh1il8r358hqq3f")))) + "0cryqnpqb3p6l9jjw27hyqd550sxlljls3ka7b9rb38hkji7b5hw")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -6157,13 +6149,13 @@ possible.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.10.0") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0nhg4bk38gzvf3mvnbqgisbbhfv1kzjld27z1z9knnlkplkiyyyv")))) + "0zh894qd1sgpjbn0wfvq6hs2dzn7y1pyicvzk2aa48y3zbidanv7")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -6183,13 +6175,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.16.1") + (version "3.16.5") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1r6hhwkqp13m022hjajzr1lnjsbai0yjhykwn0kp1f0la990a808")))) + "04vpa0a6dkkjyvvfbkmfjyaxf2ldkagi66g028qpaszd8jsk8yiv")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -6209,13 +6201,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.20.0") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1lwzfgahz8ipwli73kcfqb18y6adi129hap1gnycnj3980m54i8q")))) + "165wda1d2jagd907pnra4m3sla66icyqxvd60xpv09jl5agd5mn9")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -6247,13 +6239,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.30.2") + (version "3.30.7") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "04jris7wk2lxksrrvrjsysznsdb2k04lfgrnp18ic49sazva0hfy")))) + "1xg9w4lmn9n4hwyflxiwi6g969lcy569cg4z1x47crwwg7z7qdka")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -6302,13 +6294,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.26.1") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "039nxccg9i2an8q2wni79x8dr9p1fcfcqvih9hg9w243pczg2g3c")))) + "0if5dswkp77lyqppd0z2iyvnwag9h1gsr03707s8npcx13mzpsia")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -6434,13 +6426,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.42.0") + (version "2.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "08z8lkz3axa94wkf144a931ry6vf6cc25avi1ywr84ln2k5czz9f")))) + "0vqgd9i6y3wj4zviqwgvwgd4qj6033fg01rmx1cw9bw5i8ans42d")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -6611,13 +6603,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.26.0") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0z8spi2knwzwi10c38vr7xlvi3ah9faj7m1lka880mmxkl9cai4k")))) + "1ybi6r3bax07wlv2qcd34y5qjdvcqcfayfvlrjc39ifrkk65wv4f")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7097,6 +7089,41 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-txdb-mmusculus-ucsc-mm10-knowngene + (package + (name "r-txdb-mmusculus-ucsc-mm10-knowngene") + (version "3.4.0") + (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://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "TxDb.Mmusculus.UCSC.mm10.knownGene_" + version ".tar.gz")) + (sha256 + (base32 + "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb")))) + (properties + `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.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-bsgenome" ,r-bsgenome) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-annotationdbi" ,r-annotationdbi))) + (home-page + "http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") + (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") + (description + "This package loads a TxDb object, which is an R interface to +prefabricated databases contained in this package. This package provides +the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) +based on the knownGene track.") + (license license:artistic2.0))) + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") @@ -7223,7 +7250,7 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-qtl (package (name "r-qtl") - (version "1.39-5") + (version "1.40-8") (source (origin (method url-fetch) @@ -7231,7 +7258,7 @@ throughput genetic sequencing data sets using regression methods.") version ".tar.gz")) (sha256 (base32 - "1grwgvyv7x0dgay1858bg7qf4wk47gpnq7qkqpcda9cn0h970d6f")))) + "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp")))) (build-system r-build-system) (home-page "http://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -7347,7 +7374,7 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.0.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" @@ -7355,7 +7382,7 @@ paired-end data.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1h7di822ihgkhmmmlfbfz3c2dkjyjxl307i6mx8w0cwjqbna1kp6")))) + "1hd0r66556bxbdd82ksjklq7nfli36l4k6y88ic7kkg9873wa1nw")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr) @@ -7377,6 +7404,7 @@ paired-end data.") ("r-topgo" ,r-topgo) ("r-dt" ,r-dt) ("r-plotly" ,r-plotly) + ("r-plotrix" ,r-plotrix) ("r-motifrg" ,r-motifrg) ("r-genomation" ,r-genomation) ("r-genomicfeatures" ,r-genomicfeatures) @@ -7796,7 +7824,7 @@ may optionally be provided to further inform the peak-calling process.") `(("python2-numpy" ,python2-numpy) ("python2-scipy" ,python2-scipy) ("python2-pysam" ,python2-pysam))) - (home-page "https://code.google.com/p/pepr-chip-seq/") + (home-page "https://github.com/shawnzhangyx/PePr") (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") (description "PePr is a ChIP-Seq peak calling or differential binding analysis tool @@ -7837,17 +7865,20 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "0.6") + (version "0.9") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy")))) + "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny")) + (patches (search-patches "multiqc-fix-git-subprocess-error.patch")))) (build-system python-build-system) - (native-inputs - `(("python-nose" ,python-nose))) + (arguments + ;; Tests are to be introduced in the next version, see + ;; https://github.com/ewels/MultiQC/issues/376 + `(#:tests? #f)) (propagated-inputs `(("python-jinja2" ,python-jinja2) ("python-simplejson" ,python-simplejson) @@ -7862,3 +7893,94 @@ replacement for strverscmp.") samples into a single report. It contains modules for a large number of common bioinformatics tools.") (license license:gpl3))) + +(define-public r-chipseq + (package + (name "r-chipseq") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chipseq" version)) + (sha256 + (base32 + "115ayp82rs99iaswrx45skw1i5iacgwzz5k8rzijbp5qic0554n0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-shortread" ,r-shortread))) + (home-page "http://bioconductor.org/packages/chipseq") + (synopsis "Package for analyzing ChIPseq data") + (description + "This package provides tools for processing short read data from ChIPseq +experiments.") + (license license:artistic2.0))) + +(define-public r-copyhelper + (package + (name "r-copyhelper") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "http://bioconductor.org/packages/release/" + "data/experiment/src/contrib/CopyhelpeR_" + version ".tar.gz")) + (sha256 + (base32 + "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) + (properties `((upstream-name . "CopyhelpeR"))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/CopyhelpeR/") + (synopsis "Helper files for CopywriteR") + (description + "This package contains the helper files that are required to run the +Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content +and mappability files for the reference genomes hg18, hg19, hg38, mm9 and +mm10. In addition, it contains a blacklist filter to remove regions that +display copy number variation. Files are stored as GRanges objects from the +GenomicRanges Bioconductor package.") + (license license:gpl2))) + +(define-public r-copywriter + (package + (name "r-copywriter") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopywriteR" version)) + (sha256 + (base32 + "1bwwnsyk7cpgwkagsnn5mv6fv233b0rkhjvbadrh70h8m4anawfj")))) + (properties `((upstream-name . "CopywriteR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-chipseq" ,r-chipseq) + ("r-copyhelper" ,r-copyhelper) + ("r-data-table" ,r-data-table) + ("r-dnacopy" ,r-dnacopy) + ("r-futile-logger" ,r-futile-logger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/PeeperLab/CopywriteR") + (synopsis "Copy number information from targeted sequencing") + (description + "CopywriteR extracts DNA copy number information from targeted sequencing +by utilizing off-target reads. It allows for extracting uniformly distributed +copy number information, can be used without reference, and can be applied to +sequencing data obtained from various techniques including chromatin +immunoprecipitation and target enrichment on small gene panels. Thereby, +CopywriteR constitutes a widely applicable alternative to available copy +number detection tools.") + (license license:gpl2))) |