Chromatin analysis module

Multimodal datasets, in MuData format

Pipeline to process sc-ATAC data with pyCistopic

Code for Walker, Saunders, Rai et al., (2021).

Official – El Arkhe

A spin-off devel ArchR repo, for chromatin accessibility analysis

Multiome (RNA+ATAC from same cell) data generated by Qinyu Zhang in David Bryder's lab. Paper here: https://doi.org/10.7554/eLife.91826.2

Accompanying code for analysis of manuscript in Nature Aging: Implications of stress-induced gene expression for hematopoietic stem cell aging studies

Automated sample QC and processing for RNA/ATAC multiome

A nextflow workflow that wraps SAMap

10x multiome sequencing of 3 independent differentiations of stem-cells to pancreatic islets

WDLized Cell Ranger ARC