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04/04: gnu: Add python-scanpy.
From: |
Ricardo Wurmus |
Subject: |
04/04: gnu: Add python-scanpy. |
Date: |
Wed, 29 Aug 2018 11:06:21 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit c7fe888b424faec05a0d55e8b9321d6852ffb1f2
Author: Ricardo Wurmus <address@hidden>
Date: Wed Aug 29 17:05:46 2018 +0200
gnu: Add python-scanpy.
* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
---
gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cb3c4bc..3c300e4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13458,3 +13458,39 @@ conversions, region filtering, FASTA sequence
extraction and more.")
spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA)
in RNA-seq data.")
(license license:gpl3))))
+
+(define-public python-scanpy
+ (package
+ (name "python-scanpy")
+ (version "1.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "scanpy" version))
+ (sha256
+ (base32
+ "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-anndata" ,python-anndata)
+ ("python-igraph" ,python-igraph)
+ ("python-numba" ,python-numba)
+ ("python-joblib" ,python-joblib)
+ ("python-natsort" ,python-natsort)
+ ("python-networkx" ,python-networkx)
+ ("python-statsmodels" ,python-statsmodels)
+ ("python-scikit-learn" ,python-scikit-learn)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-pandas" ,python-pandas)
+ ("python-scipy" ,python-scipy)
+ ("python-seaborn" ,python-seaborn)
+ ("python-h5py" ,python-h5py)
+ ("python-tables" ,python-tables)))
+ (home-page "http://github.com/theislab/scanpy")
+ (synopsis "Single-Cell Analysis in Python.")
+ (description "Scanpy is a scalable toolkit for analyzing single-cell gene
+expression data. It includes preprocessing, visualization, clustering,
+pseudotime and trajectory inference and differential expression testing. The
+Python-based implementation efficiently deals with datasets of more than one
+million cells.")
+ (license license:bsd-3)))