python-bbknn
Batch balanced KNN
BBKNN is a batch effect removal tool that can be directly used in the Scanpy workflow. It serves as an alternative to scanpy.api.pp.neighbors(), 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.
- Versions: 1.6.0
- Website: https://github.com/Teichlab/bbknn
- Licenses: Expat
- Package source: gnu/packages/bioinformatics.scm
- Builds: See build status
- Issues: See known issues
Installation
Install the latest version of python-bbknn as follows:
guix install python-bbknn
Or install a particular version:
guix install python-bbknn@1.6.0
You can also install packages in augmented, pure or containerized environments for development or simply to try them out without polluting your user profile. See the guix shell documentation for more information.
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