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dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=qMXi6J3w; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 1F0FF2F8B5 X-Spam-Score: -1.17 X-TUID: AmGHEI6ot5Gn * gnu/packages/bioinformatics.scm (python-cell2cell): New variable. --- gnu/packages/bioinformatics.scm | 64 +++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 89f8041d56..6dbbc26eac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1298,6 +1298,70 @@ (define-public python-biofluff experiments.") (license license:expat))) +(define-public python-cell2cell + (package + (name "python-cell2cell") + (version "0.6.8") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/earmingol/cell2cell") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hwww0rcv8sc4k312n4d0jhbyix1jjqgv5djg25bw8127q5iym3s")) + (modules '((guix build utils))) + (snippet '(begin + (substitute* "cell2cell/plotting/factor_plot.py" + (("from statannotations.Annotator import Annotator") + "") + (("if statistical_test is not None") + "if False")) + (substitute* "setup.py" + (("'statannotations',") + "")) + (substitute* "setup.py" + (("matplotlib >= 3.2.0,<=3.5.1") + "")) + (substitute* "setup.py" + (("'gseapy == 1.0.3'") + "'gseapy'")))))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;There are no tests + #:phases '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-gseapy + python-kneed + python-matplotlib + python-networkx + python-numpy + python-openpyxl + python-pandas + python-scikit-learn + python-scipy + python-seaborn + python-statsmodels + python-scanpy + python-seaborn + python-tensorly + python-tqdm + python-umap-learn + python-xlrd)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/earmingol/cell2cell") + (synopsis "Python library for cell communication analysis") + (description + "Cell2cell is a Python library for cell communication analysis. +This is a method to calculate, visualize and analyze communication +between cell types. Cell2cell is suitable for single-cell RNA sequencing +(scRNA-seq) data.") + (license license:bsd-3))) + (define-public python-cellbender (package (name "python-cellbender") base-commit: a7d9cd742c3149bb014db95f88d1158d590bc124 -- 2.34.1