Bioconductor Scraper

Scrape Bioconductor R package metadata. Search packages by keyword, filter by biocViews category (e.g. "RNASeq", "Sequencing", "Microarray"), or fetch specific packages by name — get version, title, description, author, maintainer, license, dependencies, and more.

Features

• Search packages by keyword across name, title, and description
• Filter by biocViews category (e.g. "RNASeq", "GenomicData", "Sequencing")
• Fetch specific packages by exact name
• Extracts: name, version, title, description, biocViews, author, maintainer, license, depends, imports, suggests, URL, bug report link
• Uses official Bioconductor JSON API — no authentication required
• Covers the full Bioconductor release repository (2,000+ packages)

Input

Field	Type	Description	Default
mode	String (select)	searchPackages or getByName	searchPackages
searchQuery	String	Keyword search in name/title/description	RNA-seq
packageNames	Array of strings	Exact package names for getByName mode	[]
biocViews	String	Filter by biocViews category	(none)
maxItems	Integer (1–1000)	Maximum number of records to return	10

Mode: searchPackages

Search Bioconductor packages whose name, title, or description contains the query string (case-insensitive). Optionally combine with a biocViews filter.

Example input:

{
  "mode": "searchPackages",
  "searchQuery": "RNA-seq",
  "maxItems": 20
}

With biocViews filter:

{
  "mode": "searchPackages",
  "biocViews": "Sequencing",
  "maxItems": 50
}

Mode: getByName

Fetch specific packages by their exact Bioconductor package name (case-insensitive).

Example input:

{
  "mode": "getByName",
  "packageNames": ["DESeq2", "edgeR", "limma"],
  "maxItems": 10
}

Output

Each record contains:

Field	Type	Description
packageName	String	Bioconductor package name
version	String	Current release version
title	String	Short package title
description	String	Full package description
biocViews	Array	Bioconductor category tags
author	String	Package author(s) with roles
maintainer	String	Current maintainer with email
license	String	License type
depends	Array	Hard dependencies
imports	Array	Imported packages
suggests	Array	Optional suggested packages
vignettes	Array	Vignette builder tools
url	String	Project URL
bugReports	String	Bug tracker URL
sourceUrl	String	Bioconductor package page URL
recordType	String	Always "package"
scrapedAt	String	ISO 8601 timestamp

Sample Output Record

{
  "packageName": "DESeq2",
  "version": "1.42.0",
  "title": "Differential gene expression analysis based on the negative binomial distribution",
  "description": "Estimate variance-mean dependence in count data from RNA-Seq experiments, and test for differential expression based on a model using the negative binomial distribution.",
  "biocViews": ["RNASeq", "Sequencing", "DifferentialExpression", "GeneExpression", "Transcriptomics"],
  "author": "Michael Love [aut, cre], Simon Anders [aut], Wolfgang Huber [aut]",
  "maintainer": "Michael Love <michaelisaiahlove@gmail.com>",
  "license": "LGPL (>= 3)",
  "depends": ["R", "S4Vectors", "IRanges", "GenomicRanges", "SummarizedExperiment"],
  "imports": ["BiocGenerics", "Biobase", "locfit", "ggplot2"],
  "suggests": ["knitr", "rmarkdown", "testthat"],
  "vignettes": ["knitr"],
  "url": "https://github.com/thelovelab/DESeq2",
  "bugReports": "https://github.com/thelovelab/DESeq2/issues",
  "sourceUrl": "https://bioconductor.org/packages/release/bioc/html/DESeq2.html",
  "recordType": "package",
  "scrapedAt": "2026-05-30T12:00:00+00:00"
}

Data Source

Data is sourced from the official Bioconductor packages JSON API. No authentication is required.

biocViews Categories

Common biocViews categories you can use as filters:

• RNASeq — RNA sequencing analysis
• Sequencing — Next-generation sequencing
• Microarray — Microarray data analysis
• GenomicData — Genomic data representation
• Infrastructure — Core infrastructure packages
• DifferentialExpression — Differential expression analysis
• Proteomics — Proteomics data
• Metabolomics — Metabolomics data
• SingleCell — Single-cell RNA sequencing
• Epigenetics — Epigenetic data analysis
• VariantAnnotation — Genetic variant annotation

FAQs

Q: How many Bioconductor packages are available? A: The Bioconductor release repository contains over 2,200 software packages.

Q: What Bioconductor version does this use? A: The actor scrapes the current release (3.18). Data includes packages from bioconductor.org/packages/release/bioc/.

Q: Can I search across multiple biocViews categories? A: The biocViews filter accepts one category at a time. Use searchQuery for broader keyword searches.

Q: Are annotation and experiment packages included? A: The actor focuses on the main software package repository. Annotation and experiment data packages are not included.

Q: What does "depends" vs "imports" vs "suggests" mean? A: These are standard R package dependency levels. depends are hard dependencies loaded on attach; imports are used internally; suggests are optional extras for examples or vignettes.

Q: Why are version constraints removed from dependency lists? A: The actor strips version constraints (e.g. R (>= 4.0)) to provide clean package name lists. The full constraint information is in the package description page.