EpiScanpy: integrated single-cell epigenomic analysis

All files below are in "h5ad" format, which can be opened by the Python package AnnData (see https://anndata.readthedocs.io/en/latest). The files are organized as:

1. Single-nucleus methylcytosine sequencing (snmC-seq) of neurons from the frontal cortex of young adult mouse brains from Luo et al., 2017. The files are the preprocessed input for EpiScanpy for multiple CG imputed feature spaces, 100k base pair windows, enhancers, gene bodies, promoters and CH gene bodies.
- processed_enhancers_CG_luo_et_al_nov2020_paper_resubmission.h5ad
- processed_genebodies_CG_luo_et_al_nov2020_paper_resubmission.h5ad
- processed_genebodies_CH_luo_et_al_nov2020_paper_resubmission.h5ad
- processed_promoter_CG_luo_et_al_nov2020_paper_resubmission.h5ad
- processed_windows_CG_luo_et_al_nov2020_paper_resubmission.h5ad
 

2. Single cell ATAC sequencing (scATAC-seq) from 10X Genomics, preprocessed peak count matrix of Next GEM v1.1 10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor. Peak matrices of Next GEM v1.1 10k PBMCs and whole blood fresh data (GEO:GSE129785) from Satpathy et al. 2019 (Greenleaf's lab). Concatenated 5000bp matrix of Fresh cortex from adult mouse brain (P50) from 10X Genomics and CEMBA180312_3B mouse brain sample from Fang et al. 2019.
- atac_pbmc_10k_nextgem_fragments_macs2_peaks_outter_all_chrom.h5ad
- atac_pbmc_10k_nextgem_fragments_merged_peaks_for_integration_greenleaf_outter_all_chrom.h5ad
- raw_greenleaf_pre_integration_oct_2020.h5ad (Satpathy et al. 2019)
- preprocessed_10x_genomics_5k_adulte_mouse_brain_Fang_et_al_2019_CEMBA180312_3B_5kb_windows.h5ad