EpiScanpy (Epigenomics single cell analysis in python) 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). For more information, read scanpy documentation.
The documentation for epiScanpy is available here. If epiScanpy is useful to your research, consider citing epiScanpy.
Here you can find the analysis of bone marrow cell types measured using scATAC-seq (data from Cusanovich et al. 2018), as well as brain cell types measured using scATAC-seq (from Cusanovich et al. 2018), PBMC data from Satpathy et al. 2019 as well as 10X 10k cells PBMC data. Additionally we provide data integration processing scripts to integrate brain sample from 10X and Fang et al. 2018 as well as PBMC data from 10x 10k PBMC cells and PBMC data from Satpathy et al. 2019. Also, we provide the scripts used for the benchmarking of epiScanpy to other scATACseq data processing methods using https://github.com/pinellolab/scATAC-benchmarking implementation (Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E. Vinyard, Sara P. Garcia, Kendell Clement, Miguel A. Andrade-Navarro, Jason D. Buenrostro & Luca Pinello. Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biology 20, 241 (2019).). You can also find the dockerfile for installation.
Due to the large size of the data, they are not directly available on Github. Send an email to anna.danese@helmholtz-muenchen.de and we will make them available.