Analysis code related to work presented in Schiroli et al. (2023)
Code repository:
01_getCountsSE.R - Code for deriving single cell reads-in-peaks (RIPs) counts matrix from individual samples' fragments files for single cell ATAC-seq (scATAC-seq) data
02_filtCountsSEQC.R - Code for QC-filtering of single cell data
03_runCisTopics.R - Code for running cisTopics on scATAC-seq data
04_clustCells.R - Code for dimensionality reduction and clustering application to the scATAC-seq data
05_runchromVAR.R - Code for running chromVAR TF motif accessibility analysis using scTAC-seq data
06_DESeq.R - Code for running differential peak accessibility analysis between Tet2KO and WT GMP cells using DESeq2