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Genrich — peak caller for genomic enrichment assays (ChIP-seq and ATAC-seq) with built-in support for multiple biological replicates via Fisher's method, multimapping reads with fractional pileup coun
Use with AI
Install the MCP server or CLI to instantly fetch Genrich documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/genrich
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
1 shared topic • 1 shared operation
Use when working with chipseeker — chIPseeker — R/Bioconductor package
1 shared topic • 1 shared operation
ENCODE ChIP-seq pipeline — official ENCODE DCC WDL/Cromwell pipeline for transcription factor (TF) and histone mark ChIP-seq analysis. Handles adapter trimming (Trimmomatic), alignment (Bowtie2/BWA),
1 shared topic • 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
1 shared topic • 1 shared operation
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 (
1 shared topic • 1 shared operation