Run the snATAC_pipeline_CB.py
(for combinatorial indexing single cell ATAC-seq) or snATAC_pipeline_10X.py
(for droplet-based 10X single cell ATAC-seq) pipeline to generate input matrices for clustering.
Use the T1D_merged_snATAC.ipynb
notebook using the input matrices to cluster cells.
R
trim_galore
bwa
samtools
bedtools
picard
macs2
numpy
pandas
scipy
matplotlib
seaborn
pysam
rpy2
scanpy
anndata
Matrix
harmony