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EpiScanpy – Epigenomics single cell analysis in python

EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018) [Wolf18]. For more information, read scanpy documentation.

The documentation for epiScanpy is available here. If epiScanpy is useful to your research, consider citing epiScanpy.

Report issues and access the code on GitHub.


Also see the release notes of scanpy.

Also see the release notes of anndata.

Version 0.2.0 August 7, 2020

This release deal with the compatibility problems with the latest version of scanpy. Additionally, it contains new features to build quick custom count matrices (bld_mtx_fly), to convert snap into h5ad files (snap2anndata) or build gene activity matrices (geneactivity).

Version 0.1.8 November 5, 2019

Release new processing function & quality controls.

Version 0.1.7 November 5, 2019

Release for SCOG epiScanpy Hackathon in Saarbrucken.

This version is not fully compatible with previous version.

Version 0.1.0 May 10, 2019

Initial release.