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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 53 |
1 files changed, 53 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 65da049c79..7e6d76e022 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13615,3 +13615,56 @@ fasta subsequences.") storage format, called @code{cool}, used to store genomic interaction data, such as Hi-C contact matrices.") (license license:bsd-3))) + +(define-public python-hicexplorer + (package + (name "python-hicexplorer") + (version "2.1.4") + (source + (origin + ;; The latest version is not available on Pypi. + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/HiCExplorer.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'loosen-up-requirements + (lambda _ + (substitute* "setup.py" + (("==") ">=")) + #t))))) + (propagated-inputs + `(("python-biopython" ,python-biopython) + ("python-configparser" ,python-configparser) + ("python-cooler" ,python-cooler) + ("python-future" ,python-future) + ("python-intervaltree" ,python-intervaltree) + ("python-jinja2" ,python-jinja2) + ("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pybigwig" ,python-pybigwig) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy) + ("python-six" ,python-six) + ("python-tables" ,python-tables) + ("python-unidecode" ,python-unidecode))) + (home-page "http://hicexplorer.readthedocs.io") + (synopsis "Process, analyze and visualize Hi-C data") + (description + "HiCExplorer is a powerful and easy to use set of tools to process, +normalize and visualize Hi-C data. HiCExplorer facilitates the creation of +contact matrices, correction of contacts, TAD detection, A/B compartments, +merging, reordering or chromosomes, conversion from different formats +including cooler and detection of long-range contacts. Moreover, it allows +the visualization of multiple contact matrices along with other types of data +like genes, compartments, ChIP-seq coverage tracks (and in general any type of +genomic scores), long range contacts and the visualization of viewpoints.") + (license license:gpl3))) |