chipseeker

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gynecoloji / snakemake_CutandRunseq

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

quality-control snakemake homer epigenomics peak-calling deeptools cutandrun differential-binding chipseeker seacr motif-enrichment

Updated Jul 30, 2026
Python

gynecoloji / snakemake_ChIPseq

Star

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)

docker snakemake homer idr epigenomics macs2 peak-calling deeptools apptainer differential-binding chipseeker motif-enrichment

Updated Jul 30, 2026
Python

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