diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 47 |
1 files changed, 41 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 51640b710f..8968325e83 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") @@ -9756,11 +9791,11 @@ tasks.") (license license:expat)))) (define-public r-chromunity - (let ((commit "09fce8bc12cb84b45a6ea25bf8db6e5b75113d4f") + (let ((commit "712e56ccba64e8881dbb203546379a5c3c639bb2") (revision "1")) (package (name "r-chromunity") - (version (git-version "0.0.1" revision commit)) + (version (git-version "0.0.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -9769,12 +9804,13 @@ tasks.") (file-name (git-file-name name version)) (sha256 (base32 - "0lp0h614k8fq6h9gpbylk4chh7q6w4qda8lx03ajrpppxmg7al2d")))) + "0sdja11l7bg5rmcbp2cl226cq9qrj3r8kq5lg49zbin83hya27vh")))) (properties `((upstream-name . "chromunity"))) (build-system r-build-system) (propagated-inputs (list r-arrow r-biocgenerics + r-bsgenome-hsapiens-ucsc-hg38 r-data-table r-gchain r-genomicranges @@ -9786,7 +9822,6 @@ tasks.") r-pbmcapply r-plyr r-r6 - r-skitools r-zoo)) (home-page "https://github.com/mskilab/chromunity") (synopsis "Discovery of communities in Pore-C concatemers") @@ -17867,7 +17902,7 @@ multiple experimental contexts.") (define-public vbz-compression (package (name "vbz-compression") - (version "1.0.1") + (version "1.0.3") (source (origin (method git-fetch) @@ -17879,7 +17914,7 @@ multiple experimental contexts.") (file-name (git-file-name name version)) (sha256 (base32 - "1c6wsrnw03vsc5cfp2rdakly5xy55m9chjmy6v685yapdwirdky0")))) + "1rn5d98flvjblhj4zjpcdqqh8qlgsh5cmb13i49fnm187p03097z")))) (build-system cmake-build-system) (arguments `(#:configure-flags |