Browse Tools

Use for deterministic conversion of workflow specifications into Nextflow DSL2, Snakemake 8+, WDL 1.0, and CWL v1.2 pipelines with container-aware resource routing and validation.

Analyze bioinformatics sample metadata to auto-detect data modality, column semantics, and sequencing platform from CSV/TSV files, SRA RunTables, GEO Series Matrix files, and AnnData .obs exports. Inf

Use when working with pipeline-composer — pipeline-composer — compose

mediation — R package for causal mediation analysis implementing parametric and non-parametric methods. Core function mediate() estimates average causal mediation effects (ACME), average direct effect

Benchmark and compare bioinformatics tools for a given analysis task using published benchmark data (accuracy, runtime, memory), PrecisionFDA and CAMI challenge results, bc7score community metrics, an

Hymenoptera Genome Database (HGD) — community resource for ant, bee, and wasp genome sequences, gene annotations, and comparative genomics. Provides BLAST search, genome browsers (JBrowse), gene expre

Compound Discoverer routing skill for metabolomics and lipidomics LC-MS/MS data processing and compound identification using Thermo Fisher Scientific Compound Discoverer software. Use this skill when

DMRcate — R/Bioconductor package for identifying differentially methylated regions (DMRs) from Illumina Infinium arrays (450K, EPIC, EPICv2) and whole genome bisulfite sequencing (WGBS/RRBS) data. Use

HMDB tools routing skill for metabolomics and lipidomics compound annotation using the Human Metabolome Database. Use this skill when users mention HMDB, Human Metabolome Database, HMDB IDs, HMDB REST

'Use when working with bio-tool-search — bio-tool-search — search 47,000+

DMU skill for multivariate mixed-model analyses in animal breeding and veterinary genomics. Use this skill when users ask about DMU driver files, dmu1 plus dmuai/dmu4/dmu5/rjmc module selection, AI-RE

Use when working with validate-paper-tools — an MCP tool that verifies whether bioinformatics tools or methods referenced in a scientific paper exist in the 25K+ BioContext7 registry, checks their mai

UniProt REST API tools — programmatic access to UniProtKB, UniRef, and UniParc protein databases via the REST API at rest.uniprot.org. Supports protein search, entry retrieval, sequence download, ID m

A collection of tools for accessing, analyzing, and downloading data from the Biobank Japan project. Provides functionalities for querying phenotypes, genotypes, and other omics data.

Route workflow linting and syntax checks for Nextflow DSL2, Snakemake, WDL, and CWL. Trigger phrases: validate-workflow-syntax, workflow validation, nextflow syntax, snakemake lint, wdl validate, cwl

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