peak-calling

ChIP-seq peak-calling, QC and differential analysis pipeline.

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

The ChIP-Seq peak calling algorithm using convolution neural networks

Single-cell APA peak calling and poly(A) tail analysis from scRNA-seq. Detects polyadenylation sites, quantifies 3'UTR length switching, and compares APA usage across cell clusters and samples.

ChIP-Seq processing pipeline on snakemake

ORACLE bulk ATAC-seq pipeline (Snakemake + conda): FASTQ/SRA to differential chromatin accessibility, peak annotation, TF motif enrichment & footprinting; multi-species, MultiQC.

ChIP-seq analysis: QC and contamination screening, Bowtie2 alignment, MACS2 broad peaks, DiffBind, and monaLisa/JASPAR motif enrichment, with a MultiQC report.

Multiple-replica multiple-condition ChIPSeq pipeline

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Benchmarking ChIP-seq peak callers

CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

🥇 Maximum homogeneity clustering for one-dimensional data

An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq

cell-free ChIP-seq pipeline

The MeRIP-seq data analysis tutorial is structured into four submodules, designed to comprehensively guide users through the complete workflow for RNA methylation analysis

R package for mining, calling, and importing epigenomic peaks.

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.

Merge multiple peak calling experiments into consensus peaks and a sparse consensus by sample matrix (part of MUFFIN suite).

Offline RNA, DNA, protein, single-cell and genomic interval benchmarks with a five-assay demo and traceable reports.

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).