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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2e786b3290..1214a0b708 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -570,6 +570,51 @@ resolution of binding sites through combining the information of both sequencing tag position and orientation.") (license license:bsd-3))) +(define-public miso + (package + (name "miso") + (version "0.5.3") + (source (origin + (method url-fetch) + (uri (string-append + "http://pypi.python.org/packages/source/m/misopy/misopy-" + version ".tar.gz")) + (sha256 + (base32 + "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w")) + (modules '((guix build utils))) + ;; use "gcc" instead of "cc" for compilation + (snippet + '(substitute* "setup.py" + (("^defines") + "cc.set_executables( +compiler='gcc', +compiler_so='gcc', +linker_exe='gcc', +linker_so='gcc -shared'); defines"))))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; only Python 2 is supported + #:tests? #f)) ; no "test" target + (inputs + `(("samtools" ,samtools) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-scipy" ,python2-scipy) + ("python-matplotlib" ,python2-matplotlib))) + (native-inputs + `(("python-setuptools" ,python2-setuptools))) + (home-page "http://genes.mit.edu/burgelab/miso/index.html") + (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") + (description + "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates +the expression level of alternatively spliced genes from RNA-Seq data, and +identifies differentially regulated isoforms or exons across samples. By +modeling the generative process by which reads are produced from isoforms in +RNA-Seq, the MISO model uses Bayesian inference to compute the probability +that a read originated from a particular isoform.") + (license license:gpl2))) + (define-public rseqc (package (name "rseqc") |