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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c199883829..aef9625534 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14949,6 +14949,56 @@ line, interactively explore genomic data within Jupyter environment or web browser.") (license license:gpl3+))) +(define-public scregseg + (package + (name "scregseg") + (version "0.1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BIMSBbioinfo/scregseg") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112")))) + (build-system python-build-system) + (arguments + `(#:tests? #false ; tests require network access + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-fail-to-find-sklearn + (lambda _ + ;; XXX: I have no idea why it cannot seem to find sklearn. + (substitute* "setup.py" + (("'sklearn',") ""))))))) + (native-inputs + `(("python-cython" ,python-cython))) + (propagated-inputs + `(("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy) + ("python-numpy" ,python-numpy) + ("python-hmmlearn" ,python-hmmlearn) + ("python-pandas" ,python-pandas) + ("python-numba" ,python-numba) + ("python-anndata" ,python-anndata) + ("python-scanpy" ,python-scanpy) + ("python-pybedtools" ,python-pybedtools) + ("python-pysam" ,python-pysam) + ("python-matplotlib" ,python-matplotlib) + ("python-seaborn" ,python-seaborn) + ("python-coolbox" ,python-coolbox))) + (home-page "https://github.com/BIMSBbioinfo/scregseg") + (synopsis "Single-cell regulatory landscape segmentation") + (description "Scregseg (Single-Cell REGulatory landscape SEGmentation) is a +tool that facilitates the analysis of single cell ATAC-seq data by an +HMM-based segmentation algorithm. Scregseg uses an HMM with +Dirichlet-Multinomial emission probabilities to segment the genome either +according to distinct relative cross-cell accessibility profiles or (after +collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct +cross-cluster accessibility profiles.") + (license license:gpl3+))) + (define-public r-ascat (package (name "r-ascat") |