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BEDTools — Swiss-army knife for genome arithmetic on genomic intervals. Provides intersect, merge, subtract, complement, closest, window, coverage, genomecov, slop, flank, sort, groupby, getfasta, mas
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Install the MCP server or CLI to instantly fetch BEDTools documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/bedtools
docker pull biocontainers/bedtools:unknownUse when converting Illumina BCL (Binary Base Call) files to FASTQ format, demultiplexing sequencing runs by index sequences, or trimming adapters from short-read data. Handles HiSeq, MiSeq, NextSeq,
2 shared topics • 1 shared operation
GenomicRanges — Bioconductor R package for representing, manipulating, and analyzing genomic intervals (GRanges, GRangesList). Provides operations for finding overlaps (findOverlaps, subsetByOverlaps)
2 shared topics
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 (
2 shared topics
MEME Suite — comprehensive motif analysis toolkit for DNA, RNA, and protein sequences. Provides de novo motif discovery (MEME, STREME), motif scanning (FIMO), motif comparison (TOMTOM), motif enrichme
2 shared topics
pygenometracks -- Python program and library for plotting publication-quality genome browser tracks. Generates highly customizable visualizations of bigwig, BED, GTF, bedgraph, Hi-C matrices, links/ar
2 shared topics