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MACS2 (Model-based Analysis of ChIP-Seq) — the standard peak caller for ChIP-seq and ATAC-seq experiments. Identifies transcription factor binding sites (narrow peaks), histone modification domains (b
Use with AI
Install the MCP server or CLI to instantly fetch MACS2 (Model-based Analysis of ChIP-Seq) documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/macs2
IDR (Irreproducible Discovery Rate) — statistical framework for assessing and controlling reproducibility of high-throughput sequencing experiments across biological replicates. Fits a copula mixture
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
Bracken (Bayesian Reestimation of Abundance with KrakEN) — statistical method for computing species-level abundance estimates from Kraken/Kraken2/KrakenUniq taxonomic classifications. Redistributes re
1 shared topic • 2 shared operations
Sarek — nf-core Nextflow pipeline for germline and somatic variant calling from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing data. Supports multiple variant cal
1 shared topic • 2 shared operations
sigmap is a C++ tool for signal-level alignment of nanopore sequencing data, mapping raw electrical signals (squiggles) directly to a reference genome without basecalling. Uses Dynamic Time Warping (D
1 shared topic • 2 shared operations