diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 58c0f07e87..0484ea3b0d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4491,6 +4491,50 @@ (define-public python-mudata omics data.") (license license:bsd-3))) +(define-public python-mofapy2 + (package + (name "python-mofapy2") + (version "0.7.1") + (source + (origin + ;; The tarball from PyPi doesn't include tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/bioFAM/mofapy2") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ahhnqk6gjrhyq286mrd5n7mxcv8l6040ffsawbjx9maqx8wbam0")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; cupy is an optional dependency, which + ;; itself has nonfree dependencies (CUDA) + '(list "--ignore=mofapy2/notebooks/test_cupy.py"))) + (propagated-inputs (list python-anndata + python-h5py + python-numpy + python-pandas + python-scikit-learn + python-scipy)) + (native-inputs (list python-poetry-core + python-pytest)) + (home-page "https://biofam.github.io/MOFA2/") + (synopsis "Multi-omics factor analysis") + (description "MOFA is a factor analysis model that provides a general +framework for the integration of multi-omic data sets in an unsupervised +fashion. Intuitively, MOFA can be viewed as a versatile and statistically +rigorous generalization of principal component analysis to multi-omics data. +Given several data matrices with measurements of multiple -omics data types on +the same or on overlapping sets of samples, MOFA infers an interpretable +low-dimensional representation in terms of a few latent factors. These learnt +factors represent the driving sources of variation across data modalities, +thus facilitating the identification of cellular states or disease +subgroups.") + (license license:lgpl3))) + (define-public python-pyega3 (deprecated-package "python-pyega3" python-ega-download-client))