Navid Afkhami wrote 2 years ago
(address . guix-patches@gnu.org)(name . Navid Afkhami)(address . navid.afkhami@mdc-berlin.de)
fa8a55823ad0ad4f36c81fb7d6957a80f85d434a.1692367266.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-scDamAndTools): New variable.
---
gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
Toggle diff (49 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 51640b710f..03b1e81634 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2154,6 +2154,40 @@ (define-public python-pybedtools
;; 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 unctions for processing raw scDam&T-seq data.
+A method to simultaneously measure protein-DNA interactions and transcription
+from single cells (Rooijers et al., 2019). scDam&T-seq 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")
base-commit: 1b2d43fe016848ea2ec16ff18cbc14340944fc4e
--
2.34.1