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

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

Benchmarking ChIP-seq peak callers

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

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

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

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.

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.

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

Peak Calling algorithm for Chromatin-immunoprecipitation sequencing (ChIP-seq) data

peakScout is Python program that performs reversible peak-to-gene translation for genomic peak calling results