An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
quality-controlannotationchip-seqatac-seqbulkcell-free-dnapeak-callingdifferential-accessibilitydifferential-binding
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Updated
Sep 4, 2026 - Python
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differential-accessibility
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End-to-end Snakemake ATAC-seq pipeline (spike-in-free): Bowtie2 → MACS2 → reproducible fixed-width consensus peaks + a self-contained interactive QC report, plus opt-in CTCF-anchored differential openness (DESeq2) and TF footprinting (TOBIAS). Fully containerized (Docker/Apptainer).
dockersnakemakengsatac-seqtobiasfootprintingepigenomicsmacs2peak-callingdeeptoolsapptainerdifferential-accessibility
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Updated
Jul 30, 2026 - Python
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