diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 311 |
1 files changed, 268 insertions, 43 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9b0dad9d7..0fd97b691e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> -;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> +;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; @@ -5849,14 +5849,14 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.4-5") + (version "2.4-6") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya")))) + "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6673,19 +6673,21 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0zm63kr4f4kja4qpwkzl119zzyciqj7ihajfqgfjpgb4dzaiycxp")))) + "1pxxln42kvzl38fjprg6hcnyh1kij75fpj70vwp5hp5il813aszc")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml))) + ("r-yaml" ,r-yaml) + ("r-xfun" ,r-xfun) + ("ghc-pandoc" ,ghc-pandoc))) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for @@ -6965,13 +6967,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.20.2") + (version "3.20.8") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0j5s3i33qmld9l7gs1rzpv601zxyqz711x8mq35hml088c8s99w9")))) + "0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -6993,13 +6995,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.24.2") + (version "1.24.5") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "19wgb2kcqy97pm3xgqc781id9fbmzp1hdwzkkhdzpvyf29w4n29j")))) + "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7031,13 +7033,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.34.4") + (version "3.34.8") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1vcxf9jg8xngxg5kb9bp8rw5sghpnkpj320iq309m2fp41ahsk3f")))) + "0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7086,13 +7088,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "10ra2sjn17h6gilm9iz0cygp9ijpgbirljlc4drwrnivnw9cmi2a")))) + "1wnvvhj8yjsx242y6kfr5vs8kzisa96rxl1rgnnychrrvnvnh3i1")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7164,13 +7166,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.34.1") + (version "2.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k")))) + "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7322,13 +7324,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1011r8l0k8420j31bmh4xdcp6ka5bzf4bqhip84v5b6alpkcbvmf")))) + "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7386,13 +7388,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.38.2") + (version "1.38.3") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d")))) + "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k")))) (build-system r-build-system) (arguments `(#:phases @@ -7431,13 +7433,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.30.0") + (version "1.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1khjvq1ffhqavkwf8n7bilknci60lxbg52icrcf2vnb9k8rlpghs")))) + "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7657,13 +7659,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.10.0") + (version "1.11.3") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1ddd8c9w1f1i1ga9rpbwiic8rsaws1chdxx4j38bpyaiy4zhz1ca")))) + "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8362,14 +8364,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.61") + (version "1.62") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i")))) + "0c52rp09gqphz6g5x9jzkdcsyvfrknq0dkq9saslgy8q8ap974vx")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -8467,14 +8469,14 @@ factors bound at the specific regions.") (define-public r-gkmsvm (package (name "r-gkmsvm") - (version "0.71.0") + (version "0.79.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 - "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0")))) + "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs @@ -8941,13 +8943,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "0h53w2mrjrg2n0ndi12k9j6cwclgwcgpy25nz7nyj971aisw02xn")))) + "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9311,14 +9313,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.4.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0dqfimljhrx3gac8d1k72gppx27lz8yckyb12v4604nbviw7xd3r")))) + "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9391,13 +9393,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.1.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x")) + "1yarzhbylkfk4vwp7f8710zpdglkfww2db3hmq69hjllgg80ykmw")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9434,8 +9436,8 @@ Main-Class: ModularityOptimizer\n"))) ("r-fnn" ,r-fnn) ("r-fpc" ,r-fpc) ("r-gdata" ,r-gdata) - ("r-ggjoy" ,r-ggjoy) ("r-ggplot2" ,r-ggplot2) + ("r-ggridges" ,r-ggridges) ("r-gplots" ,r-gplots) ("r-gridextra" ,r-gridextra) ("r-hmisc" ,r-hmisc) @@ -9452,6 +9454,7 @@ Main-Class: ModularityOptimizer\n"))) ("r-ranger" ,r-ranger) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) ("r-rcppprogress" ,r-rcppprogress) ("r-reshape2" ,r-reshape2) ("r-rocr" ,r-rocr) @@ -9661,14 +9664,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1i3i88lj57wvpgjf75a23msgfsjv8pr2b4j1faga276p4fsblkhj")))) + "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -9685,14 +9688,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.28.0") + (version "2.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1r14p88q3y736pkqm4pdimf1izy1xy3xgivmj3cr4dv65kjny1zk")))) + "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9806,14 +9809,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1")))) + "1vk6j0r5cczxmwbfzzkgayna66rxkfa3q2jikz649qvdiybhls40")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9975,14 +9978,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.1") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "1qix15d0wa9nspdclcawml94mng4qmr2jciv7d24py315wfsvv8p")))) + "08dsnja3g8qvqlgwhx9c9f8p8psn3qr5ddn84dhizkgglj30v2wj")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs @@ -10401,6 +10404,228 @@ problems in genomics, brain imaging, astrophysics, and data mining.") ;; Any version of the LGPL. (license license:lgpl3+))) +(define-public r-hdf5array + (package + (name "r-hdf5array") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HDF5Array" version)) + (sha256 + (base32 + "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh")))) + (properties `((upstream-name . "HDF5Array"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) + ("r-iranges" ,r-iranges) + ("r-rhdf5" ,r-rhdf5) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/HDF5Array") + (synopsis "HDF5 back end for DelayedArray objects") + (description "This package provides an array-like container for convenient +access and manipulation of HDF5 datasets. It supports delayed operations and +block processing.") + (license license:artistic2.0))) + +(define-public r-rhdf5lib + (package + (name "r-rhdf5lib") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhdf5lib" version)) + (sha256 + (base32 + "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w")))) + (properties `((upstream-name . "Rhdf5lib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-use-bundled-hdf5 + (lambda* (#:key inputs #:allow-other-keys) + (for-each delete-file '("configure" "configure.ac")) + ;; Do not make other packages link with the proprietary libsz. + (substitute* "R/zzz.R" + (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'") + "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'") + (("'%s/libhdf5.a %s/libsz.a'") + "'%s/libhdf5.a %s/libhdf5.a'")) + (with-directory-excursion "src" + (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) + (rename-file (string-append "hdf5-" ,(package-version hdf5)) + "hdf5") + (rename-file "Makevars.in" "Makevars") + (substitute* "Makevars" + (("HDF5_CXX_LIB=.*") + (string-append "HDF5_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) + (("HDF5_LIB=.*") + (string-append "HDF5_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) + (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") + (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") + ;; szip is non-free software + (("cp \\$\\{SZIP_LIB\\}.*") "") + (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}") + "PKG_LIBS = ${HDF5_LIB}\n"))) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("hdf5" ,hdf5))) + (native-inputs + `(("hdf5-source" ,(package-source hdf5)))) + (home-page "https://bioconductor.org/packages/Rhdf5lib") + (synopsis "HDF5 library as an R package") + (description "This package provides C and C++ HDF5 libraries for use in R +packages.") + (license license:artistic2.0))) + +(define-public r-beachmat + (package + (name "r-beachmat") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beachmat" version)) + (sha256 + (base32 + "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz")))) + (build-system r-build-system) + (inputs + `(("hdf5" ,hdf5))) + (propagated-inputs + `(("r-delayedarray" ,r-delayedarray) + ("r-hdf5array" ,r-hdf5array) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5lib" ,r-rhdf5lib))) + (home-page "https://bioconductor.org/packages/beachmat") + (synopsis "Compiling Bioconductor to handle each matrix type") + (description "This package provides a consistent C++ class interface for a +variety of commonly used matrix types, including sparse and HDF5-backed +matrices.") + (license license:gpl3))) + +(define-public r-singlecellexperiment + (package + (name "r-singlecellexperiment") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SingleCellExperiment" version)) + (sha256 + (base32 + "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars")))) + (properties + `((upstream-name . "SingleCellExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/SingleCellExperiment") + (synopsis "S4 classes for single cell data") + (description "This package defines an S4 class for storing data from +single-cell experiments. This includes specialized methods to store and +retrieve spike-in information, dimensionality reduction coordinates and size +factors for each cell, along with the usual metadata for genes and +libraries.") + (license license:gpl3))) + +(define-public r-scater + (package + (name "r-scater") + (version "1.6.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scater" version)) + (sha256 + (base32 + "0fp68n0xnbf90wrprqawsbilg9x7v2scp0dxb3936g20025csrdd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-ggbeeswarm" ,r-ggbeeswarm) + ("r-ggplot2" ,r-ggplot2) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-rjson" ,r-rjson) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tximport" ,r-tximport) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/davismcc/scater") + (synopsis "Single-cell analysis toolkit for gene expression data in R") + (description "This package provides a collection of tools for doing +various analyses of single-cell RNA-seq gene expression data, with a focus on +quality control.") + (license license:gpl2+))) + +(define-public r-scran + (package + (name "r-scran") + (version "1.6.7") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scran" version)) + (sha256 + (base32 + "0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-dt" ,r-dt) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-edger" ,r-edger) + ("r-fnn" ,r-fnn) + ("r-ggplot2" ,r-ggplot2) + ("r-igraph" ,r-igraph) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-s4vectors" ,r-s4vectors) + ("r-scater" ,r-scater) + ("r-shiny" ,r-shiny) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-statmod" ,r-statmod) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-viridis" ,r-viridis) + ("r-zoo" ,r-zoo))) + (home-page "https://bioconductor.org/packages/scran") + (synopsis "Methods for single-cell RNA-Seq data analysis") + (description "This package implements a variety of low-level analyses of +single-cell RNA-seq data. Methods are provided for normalization of +cell-specific biases, assignment of cell cycle phase, and detection of highly +variable and significantly correlated genes.") + (license license:gpl3))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package |