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 or analysis type. Results use exact r-un…

Bioconductor_search_packages tool specification

Tool Information:

  • Name: Bioconductor_search_packages

  • Type: BaseRESTTool

  • Description: Search Bioconductor bioinformatics R packages by keyword or analysis type. Results use exact r-universe skip pagination: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true; metadata.total_results is exact. Returns matching packages with title, description, usage count, and relevance score.

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) Packages per page (default 10, max 100)

  • offset (integer) (optional) Zero-based package offset. Continue with metadata.next_offset while metadata.has_more is true.

Example Usage:

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