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MACS2/MACS3 — Model-based Analysis of ChIP-Seq for identifying transcription factor binding sites and histone modification enrichment from ChIP-seq, ATAC-seq, and CUT&Tag data. Provides peak calling (
Use with AI
Install the MCP server or CLI to instantly fetch MACS2/MACS3 documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/macs2macs3
MEME Suite — motif-based sequence analysis toolkit for de novo motif discovery (MEME, STREME), motif enrichment testing (AME, SEA, CentriMo), motif scanning (FIMO, MAST, MCAST), motif comparison (Tomt
3 shared topics
Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short
2 shared topics • 1 shared operation
HMMRATAC — Hidden Markov Model-based peak caller for ATAC-seq chromatin accessibility data. Identifies nucleosome-free regions (NFR), mono-, di-, and tri-nucleosomal fragments using an HMM that models
2 shared topics • 1 shared operation
nf-core/chipseq — Nextflow pipeline for comprehensive ChIP-seq analysis from raw reads through peak calling and differential analysis. Automates adapter trimming, multi-aligner support (BWA, Bowtie2,
2 shared topics • 1 shared operation
WASP (Weight And SNP-based Pipeline) corrects allele-specific mapping bias in RNA-seq and ChIP-seq by SNP-masking reads that overlap heterozygous variants, remapping them, and filtering those that shi
2 shared topics • 1 shared operation