Reproducible ChIP-seq analysis pipeline for GSE107221 using Galaxy, ChIPseeker and DiffBind to identify KDM5A-regulated H3K4me3 loci.
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Aug 5, 2026 - R
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chipseeker
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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
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Jul 30, 2026 - Python
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
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Jul 30, 2026 - Python
Interactive ATAC-seq peak analysis app in R Shiny—annotation, motif enrichment, machine learning, and more. Singularity/HPC ready.
bioinformatics r shiny hpc slurm singularity atac-seq singularity-container functional-enrichment chipseeker genomics-tools
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Jan 14, 2026 - R
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