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

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.

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

🥇 Maximum homogeneity clustering for one-dimensional data

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

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

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

Comprehensive analysis pipeline for ATAC-seq data including QC, alignment, peak calling, annotation, motif analysis, and gene enrichment. Delivers key insights and reproducible results for chromatin accessibility studies.

SPP - R package for analysis of ChIP-seq and other functional sequencing data

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