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ScFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data.

ABSTRACT:

Summary

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).

Availability and implementation

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 information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Faure L

PROVIDER: S-EPMC9805561 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data.

Faure Louis L Soldatov Ruslan R Kharchenko Peter V PV Adameyko Igor I

Bioinformatics (Oxford, England) 20230101 1

<h4>Summary</h4>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).<h4>Availability and implementation</h4>scFates is released as open-source so ...[more]

PMID: 36394263

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