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| -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 ad950b4090..4ef4f6788f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2583,6 +2583,51 @@ cell types and subtypes.") and sequence consensus.") (license license:expat))) +(define-public python-cnmf + (package + (name "python-cnmf") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cnmf" version)) + (sha256 + (base32 "0aic8cwj6riykcfgl6v2x3si5z04gaknkh5a8lcyv1qh4s1gx3d3")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #f ; no tests in git checkout and PyPI archive + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-envs + (lambda _ + (setenv "MPLCONFIGDIR" "/tmp") + ;; Numba needs a writable dir to cache functions. + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (native-inputs + (list python-setuptools + python-wheel)) + (propagated-inputs + (list python-anndata + python-fastcluster + python-matplotlib + python-numba + python-numpy + python-palettable + python-pandas + python-pyyaml + python-scanpy + python-scikit-learn + python-scipy)) + (home-page "https://github.com/dylkot/cNMF") + (synopsis "Consensus NMF for scRNA-Seq data") + (description + "This tool offers a pipeline for inferring gene expression programs from +scRNA-Seq. It takes a count matrix (N cells X G genes) as input and produces +a (K x G) matrix of gene expression programs (GEPs) and a (N x K) matrix +specifying the usage of each program for each cell in the data.") + (license license:expat))) + (define-public python-cyvcf2 (package (name "python-cyvcf2") |