Bioconductor Tools

Configuration File: bioconductor_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the bioconductor_tools.json configuration file.

Available Tools

Bioconductor_get_package (Type: BaseRESTTool)

Get detailed metadata for a specific Bioconductor R package by name. Returns comprehensive inform…

Bioconductor_get_package tool specification

Tool Information:

  • Name: Bioconductor_get_package

  • Type: BaseRESTTool

  • Description: Get detailed metadata for a specific Bioconductor R package by name. Returns comprehensive information including version, description, dependencies, biocViews categories, author/maintainer, license, download statistics, GitHub stars, reverse dependencies (packages that use it), and git repository URL. Useful for evaluating packages before installation or for understanding the Bioconductor ecosystem. Use Bioconductor_search_packages first to find package names.

Parameters:

  • package_name (string) (required) Exact Bioconductor package name (case-sensitive). Examples: ‘DESeq2’, ‘edgeR’, ‘limma’, ‘Seurat’, ‘SingleCellExperiment’, ‘GenomicRanges’, ‘BiocGenerics’, ‘clusterProfiler’, ‘Rsamtools’

Example Usage:

query = {
    "name": "Bioconductor_get_package",
    "arguments": {
        "package_name": "example_value"
    }
}
result = tu.run(query)

Bioconductor_search_packages (Type: BaseRESTTool)

Search Bioconductor bioinformatics R packages by keyword, topic, or analysis type. Bioconductor p…

Bioconductor_search_packages tool specification

Tool Information:

  • Name: Bioconductor_search_packages

  • Type: BaseRESTTool

  • Description: Search Bioconductor bioinformatics R packages by keyword, topic, or analysis type. Bioconductor provides 2200+ open-source R packages for bioinformatics and computational biology covering RNA-seq, single-cell, proteomics, epigenomics, metabolomics, flow cytometry, imaging, and more. Returns matching packages with title, description, usage count, and relevance score. Powered by R-universe search index. Use this to find packages for specific bioinformatics workflows, then use Bioconductor_get_package for full details.

Parameters:

  • q (string) (required) Search query for Bioconductor packages. Can be a keyword, analysis type, or topic. Examples: ‘differential expression’, ‘single cell RNA’, ‘proteomics’, ‘ChIP-seq’, ‘methylation’, ‘variant calling’, ‘gene set enrichment’, ‘phylogenetics’, ‘metabolomics’, ‘flow cytometry’

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default: 10, max: 100)

Example Usage:

query = {
    "name": "Bioconductor_search_packages",
    "arguments": {
        "q": "example_value"
    }
}
result = tu.run(query)