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The GTEx Pipeline is a standardized RNA-seq processing pipeline for the TOPMed project. It enables reproducible and harmonized analysis of gene expression, generating aligned reads, QC metrics, and bo
Use with AI
Install the MCP server or CLI to instantly fetch Gtex Tools documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/gtex-tools
AGAT (Another Gff Analysis Toolkit) — comprehensive Perl toolkit for reading, writing, validating, fixing, and manipulating genome annotation files in GFF3, GTF, and GFF2 formats. Converts between for
2 shared topics • 2 shared operations
CellGenIT tools from the Wellcome Sanger Institute Cellular Genetics Informatics team. Suite of Python utilities for single-cell genomics including sinto (fragment file generation from BAM), cellhint
2 shared topics • 2 shared operations
Use this skill for GATK copy-number variation workflows including germline gCNV cohorts and somatic copy-ratio segmentation from WES or WGS data. Trigger on requests about CollectReadCounts, Determine
1 shared topic • 3 shared operations
ComplexHeatmap — R/Bioconductor package for creating highly customizable heatmaps with complex annotations. Supports row/column splitting, multiple annotation tracks (bar, box, point, histogram), Onco
2 shared topics • 1 shared operation
STAR-Fusion — detects candidate fusion transcripts from RNA-seq data using STAR alignments and the FusionInspector validation framework. Integrates with CTAT genome resource libraries for comprehensiv
2 shared topics • 1 shared operation