diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 100 |
1 files changed, 98 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3bf352193c..d7089959ea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3501,7 +3501,6 @@ that a read originated from a particular isoform.") (version "3.8.1551") (source (origin (method url-fetch/tarbomb) - (file-name (string-append name "-" version)) (uri (string-append "http://www.drive5.com/muscle/muscle_src_" version ".tar.gz")) @@ -6325,7 +6324,8 @@ names in their natural, rather than lexicographic, order.") (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit))) + ("r-locfit" ,r-locfit) + ("r-statmod" ,r-statmod))) ;for estimateDisp (home-page "http://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of @@ -6885,6 +6885,37 @@ dependencies between GO terms can be implemented and applied.") genome data packages and support for efficient SNP representation.") (license license:artistic2.0))) +(define-public r-bsgenome-hsapiens-1000genomes-hs37d5 + (package + (name "r-bsgenome-hsapiens-1000genomes-hs37d5") + (version "0.99.1") + (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/" + "BSgenome.Hsapiens.1000genomes.hs37d5_" + version ".tar.gz")) + (sha256 + (base32 + "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) + (properties + `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) + (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))) + (home-page + "http://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") + (synopsis "Full genome sequences for Homo sapiens") + (description + "This package provides full genome sequences for Homo sapiens from +1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") + (license license:artistic2.0))) + (define-public r-impute (package (name "r-impute") @@ -7769,6 +7800,71 @@ for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (license license:gpl2+))) +(define-public r-tximport + (package + (name "r-tximport") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tximport" version)) + (sha256 + (base32 + "1k5a7dad6zqg936s17f6cmwgqp11x24z9zhxndsgwbscgpyhpcb0")))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/tximport") + (synopsis "Import and summarize transcript-level estimates for gene-level analysis") + (description + "This package provides tools to import transcript-level abundance, +estimated counts and transcript lengths, and to summarize them into matrices +for use with downstream gene-level analysis packages. Average transcript +length, weighted by sample-specific transcript abundance estimates, is +provided as a matrix which can be used as an offset for different expression +of gene-level counts.") + (license license:gpl2+))) + +(define-public r-rhdf5 + (package + (name "r-rhdf5") + (version "2.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5" version)) + (sha256 + (base32 + "0pb04li55ysag30s7rap7nnivc0rqmgsmpj43kin0rxdabfn1w0k")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-smallhdf5 + (lambda* (#:key outputs #:allow-other-keys) + (system* "tar" "-xzvf" + "src/hdf5source/hdf5small.tgz" "-C" "src/" ) + (substitute* "src/Makevars" + (("^.*cd hdf5source &&.*$") "") + (("^.*gunzip -dc hdf5small.tgz.*$") "") + (("^.*rm -rf hdf5.*$") "") + (("^.*mv hdf5source/hdf5 ..*$") "")) + (substitute* "src/hdf5/configure" + (("/bin/mv") "mv")) + #t))))) + (propagated-inputs + `(("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("perl" ,perl) + ("zlib" ,zlib))) + (home-page "http://bioconductor.org/packages/rhdf5") + (synopsis "HDF5 interface to R") + (description + "This R/Bioconductor package provides an interface between HDF5 and R. +HDF5's main features are the ability to store and access very large and/or +complex datasets and a wide variety of metadata on mass storage (disk) through +a completely portable file format. The rhdf5 package is thus suited for the +exchange of large and/or complex datasets between R and other software +package, and for letting R applications work on datasets that are larger than +the available RAM.") + (license license:artistic2.0))) + (define-public emboss (package (name "emboss") |