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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 35 |
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3e8fd887ee..2669942438 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2154,6 +2154,41 @@ Python.") ;; licensed lgpl2.1+ (license (list license:expat license:lgpl2.1+)))) +(define-public python-scdamandtools + (package + (name "python-scdamandtools") + (version "1.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KindLab/scDamAndTools") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mblw6cn5jqik6ky8cv7ry99z6jm1i4r71pzdfl398vrwbda65gd")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) ;there are none + (propagated-inputs (list python-h5py + python-numpy + python-sortedcontainers + python-pandas + python-pysam + python-tqdm)) + (native-inputs (list python-cython python-pytest)) + (home-page "https://github.com/KindLab/scDamAndTools") + (synopsis "Functions for processing raw scDam&T-seq data") + (description + "This is a set of functions for processing raw scDam&T-seq data. +scDam&T-seq is a method to simultaneously measure protein-DNA interactions and +transcription from single cells (Rooijers et al., 2019). It combines a +DamID-based method to measure protein-DNA interactions and an adaptation of +CEL-Seq to measure transcription. The starting point of the workflow is raw +sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq +counts.") + (license license:expat))) + (define-public python-bioframe (package (name "python-bioframe") |