An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
An R/Bioconductor package for DamID differential binding, gene transcription and chromatin accessibility analysis.
Reproducible Snakemake workflow for spike-in–normalized ATAC-seq — concatenated-genome alignment, MACS2 peaks, a consensus fragment-count matrix, an interactive QC report, and DESeq2 differential binding. Docker/Apptainer-ready.
Reproducible Snakemake workflow for paired-end CUT&RUN (no spike-in): MACS2 + SEACR peak calling with matched IgG/Input controls, mode-aware consensus count matrices, ENCODE-grade QC, and opt-in DESeq2 differential binding + ChIPseeker/HOMER downstream analysis
Reproducible Snakemake ChIP-seq pipeline: Bowtie2 → MACS2 (narrow/broad, input/IgG control) → IDR & consensus peaks → ENCODE-grade QC → differential binding, peak annotation & motif enrichment. Containerized (Docker/Apptainer)
Which normalization method recovers a genome-wide change in CUT&RUN signal? A Nextflow benchmark scored against a dataset with known ground truth.
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