I am wondering if there is a comprehensive Bioconductor tool with detailed workflow for ATACseq data analysis?
ATACseqQC is good for ATACseq data post-alignment quality control. For ATAC-seq data analysis workflow, see https://informatics.fas.harvard.edu/atac-seq-guidelines.html. For a pipeline, see esATAC: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061683/.
Thank you Haibo for your quick answer! However,
Error in atacPipe2(case = list(fastqInput1 = system.file(package = "esATAC", :
this function is still under developing
The DiffBind package vignette shows the workflow for obtaining a count matrix and performing a differential analysis of ATAC-seq data.
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