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This skill provides tools for working with data from the Trans-Omics for Precision Medicine (TOPMed) program. It includes capabilities for quality control, analysis, and visualization of large-scale g
Use with AI
Install the MCP server or CLI to instantly fetch TOPMed Tools documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/topmed-tools
HiCExplorer — comprehensive toolkit for Hi-C chromosome conformation capture data analysis, quality control, normalization, and visualization. Provides hicBuildMatrix (contact matrix construction), hi
1 shared topic • 2 shared operations
IGV (Integrative Genomics Viewer) — high-performance Java desktop application for interactive visualization and exploration of genomic data. Supports BAM/CRAM alignments, VCF variants, BED/GFF annotat
1 shared topic • 2 shared operations
MAGeCK-VISPR — comprehensive CRISPR screen analysis framework combining MAGeCK statistical testing (RRA and MLE algorithms) with VISPR interactive visualization. Supports sgRNA count generation from F
1 shared topic • 2 shared operations
PLINK 1.9/2 — high-performance command-line toolset for whole-genome association analysis, population stratification, identity-by-descent, linkage disequilibrium computation, and genotype data managem
1 shared topic • 2 shared operations
WiggleTools — command-line toolkit for streaming arithmetic and set operations on genomic signal tracks stored in Wiggle, BigWig, BedGraph, and BAM/CRAM formats. Computes sums, means, products, log tr
1 shared topic • 2 shared operations