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Broad Institute tools — access Terra cloud genomics platform, GSEA/MSigDB gene set enrichment analysis, GenePattern workflow server, Picard sequencing utilities, and FireBrowse TCGA data portal progra
Use with AI
Install the MCP server or CLI to instantly fetch Broad Institute Tools documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/broad
Maftools — R package for analyzing somatic mutations from cancer sequencing (MAF files). Provides oncoplots for mutation visualization, clonality analysis, tumor burden estimation, mutational signatur
3 shared topics • 1 shared operation
medaka -- neural network-based tool from Oxford Nanopore Technologies for creating consensus sequences and calling variants from nanopore sequencing data. Polishes draft assemblies from Flye, miniasm,
3 shared topics • 1 shared operation
Use when working with Kilosort — the GPU-accelerated spike sorting software for high-density extracellular electrophysiology recordings. Covers Kilosort4 (Python, PyTorch-based), probe/channel map con
3 shared topics
Use when working with SpikeInterface — the unified Python framework for extracellular electrophysiology spike sorting. Covers loading recordings from 30+ formats (NWB, OpenEphys, Maxwell, Intan, MDA,
3 shared topics
Telomere biology toolkit for measuring telomere length from sequencing data, analyzing telomere repeat content, detecting ALT (Alternative Lengthening of Telomeres) pathways, and studying telomere str
3 shared topics