Bioconductor Scraper

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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

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:

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.