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Use when working with VAST-TOOLS for alternative splicing analysis in RNA-seq data. Routes to references and scripts for VASTDB setup, splicing event quantification (PSI/PIR), differential splicing wi
Use with AI
Install the MCP server or CLI to instantly fetch VAST-TOOLS documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/vast-tools
PCAWG (Pan-Cancer Analysis of Whole Genomes) pipelines — standardized bioinformatics workflows from the ICGC-TCGA Pan-Cancer consortium for whole-genome somatic analysis of cancer samples. Includes al
3 shared topics • 2 shared operations
Use when working with nf-core/rnafusion — a Nextflow pipeline for RNA fusion gene detection and quantification. Detects fusion transcripts from RNA-seq data using up to six callers (STAR-Fusion, Arrib
3 shared topics • 1 shared operation
Use when integrating R and Python with reticulate: importing Python modules from R, declaring Python dependencies with py_require(), selecting Python environments (use_python/use_virtualenv/use_condae
3 shared topics • 1 shared operation
gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr
2 shared topics • 2 shared operations
IsoformSwitchAnalyzeR — R/Bioconductor package for detecting, annotating, and visualizing isoform switches with functional consequences from RNA-seq data. Integrates with Salmon, kallisto, StringTie,
2 shared topics • 2 shared operations