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04/04: gnu: Add python-bbknn.
From: |
guix-commits |
Subject: |
04/04: gnu: Add python-bbknn. |
Date: |
Thu, 28 Mar 2019 22:56:08 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit e9d4409bab594b3c28f7e74cfdcace7d1a7538c6
Author: Ricardo Wurmus <address@hidden>
Date: Fri Mar 29 03:54:46 2019 +0100
gnu: Add python-bbknn.
* gnu/packages/bioinformatics.scm (python-bbknn): New variable.
---
gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a0b44e5..c647d48 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13340,6 +13340,38 @@ Python-based implementation efficiently deals with
datasets of more than one
million cells.")
(license license:bsd-3)))
+(define-public python-bbknn
+ (package
+ (name "python-bbknn")
+ (version "1.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "bbknn" version))
+ (sha256
+ (base32
+ "1qgdganvj3lyxj84v7alm23b9vqhwpn8z0115qndpnpy90qxynwz"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-annoy" ,python-annoy)
+ ("python-cython" ,python-cython)
+ ("python-faiss" ,python-faiss)
+ ("python-numpy" ,python-numpy)
+ ("python-scanpy" ,python-scanpy)))
+ (home-page "https://github.com/Teichlab/bbknn")
+ (synopsis "Batch balanced KNN")
+ (description "BBKNN is a batch effect removal tool that can be directly
+used in the Scanpy workflow. It serves as an alternative to
address@hidden()}, with both functions creating a neighbour
+graph for subsequent use in clustering, pseudotime and UMAP visualisation. If
+technical artifacts are present in the data, they will make it challenging to
+link corresponding cell types across different batches. BBKNN actively
+combats this effect by splitting your data into batches and finding a smaller
+number of neighbours for each cell within each of the groups. This helps
+create connections between analogous cells in different batches without
+altering the counts or PCA space.")
+ (license license:expat)))
+
(define-public gffcompare
(let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41")
(revision "1"))