scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 36394263.
- Also identified by DOI 10.1093/bioinformatics/btac746 and PMC identifier 9805561.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
scFates provides an extensive toolset for the analysis of dynamic trajectories comprising tree learning, feature association testing, branch differential expression and with a focus on cell biasing and fate splits at the level of bifurcations. It is meant to be fully integrated into the scanpy ecosystem for seamless analysis of trajectories from single-cell data of various modalities (e.g. RNA and ATAC). scFates is released as open-source software under the BSD 3-Clause 'New' License and is available from the Python Package Index at https://pypi.org/project/scFates/. The source code is available on GitHub at https://github.com/LouisFaure/scFates/. Code reproduction and tutorials on published datasets are available on GitHub at https://github.com/LouisFaure/scFates_notebooks. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Ecosystem
- Software