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)
Reproducible ChIP-seq analysis pipeline for GSE107221 using Galaxy, ChIPseeker and DiffBind to identify KDM5A-regulated H3K4me3 loci.
Interactive ATAC-seq peak analysis app in R Shiny—annotation, motif enrichment, machine learning, and more. Singularity/HPC ready.
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