# Bioconductor Scraper (`crawlerbros/bioconductor-scraper`) Actor

Scrape Bioconductor R package metadata - title, description, biocViews categories, author, maintainer, license, dependencies, and more. Search by keyword or biocViews category, or fetch specific packages by name.

- **URL**: https://apify.com/crawlerbros/bioconductor-scraper.md
- **Developed by:** [Crawler Bros](https://apify.com/crawlerbros) (community)
- **Categories:** Developer tools, Automation
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $3.00 / 1,000 results

This Actor is paid per event and usage. You are charged both the fixed price for specific events and for Apify platform usage.
Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have.

Learn more: https://docs.apify.com/actors/running/actors-in-store.md#pay-per-event

## What's an Apify Actor?

Actors are web data automations that power AI and operations. They run on the Apify platform to scrape websites, process data, connect APIs, and automate workflows.
In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours,
and optionally produces a well-defined JSON output, datasets with results, or files in key-value store.
In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server.
Actors are written with capital "A".

## How to integrate an Actor?

If asked about integration, you help developers integrate Actors into their projects.
You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready.
The best way to integrate Actors is as follows.

- **AI agents and MCP clients** — the [Apify MCP server](https://docs.apify.com/integrations/mcp.md) at `https://mcp.apify.com` (remote, streamable HTTP, OAuth on first use).
- **Agentic workflows and local Actor development** — [Agent Skills](https://apify.com/.well-known/agent-skills/index.json) with the [Apify CLI](https://docs.apify.com/cli/docs.md): `npm install -g apify-cli`, then `apify login`.
- **JavaScript/TypeScript projects** — the official [JS/TS client](https://docs.apify.com/api/client/js/docs.md): `npm install apify-client`.
- **Python projects** — the official [Python client](https://docs.apify.com/api/client/python/docs.md): `pip install apify-client`.
- **Any other language** — the [REST API](https://docs.apify.com/api/v2.md).

For usage examples, see the [API](#api) section below.

For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt).

# README

## Bioconductor Scraper

Scrape [Bioconductor](https://bioconductor.org/) 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:**

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

**With biocViews filter:**

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

#### Mode: getByName

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

**Example input:**

```json
{
  "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

```json
{
  "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](https://bioconductor.org/packages/json/3.18/bioc/packages.json). 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.

# Actor input Schema

## `mode` (type: `string`):

What to fetch: search packages by keyword/category, or get specific packages by exact name.

## `searchQuery` (type: `string`):

Keyword to search in package name, title, or description (mode=searchPackages).

## `packageNames` (type: `array`):

List of exact Bioconductor package names to fetch (mode=getByName), e.g. \["DESeq2", "edgeR", "limma"].

## `biocViews` (type: `string`):

Filter by biocViews category (e.g. "Sequencing", "GenomicData", "Microarray", "RNASeq"). Case-insensitive exact match.

## `maxItems` (type: `integer`):

Maximum number of package records to return.

## Actor input object example

```json
{
  "mode": "searchPackages",
  "searchQuery": "RNA-seq",
  "maxItems": 10
}
```

# Actor output Schema

## `packages` (type: `string`):

Dataset containing all scraped Bioconductor package records.

# API

You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup.

## JavaScript example

```javascript
import { ApifyClient } from 'apify-client';

// Initialize the ApifyClient with your Apify API token
// Replace the '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "mode": "searchPackages",
    "searchQuery": "RNA-seq",
    "maxItems": 10
};

// Run the Actor and wait for it to finish
const run = await client.actor("crawlerbros/bioconductor-scraper").call(input);

// Fetch and print Actor results from the run's dataset (if any)
console.log('Results from dataset');
console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`);
const { items } = await client.dataset(run.defaultDatasetId).listItems();
items.forEach((item) => {
    console.dir(item);
});

// 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs

```

## Python example

```python
from apify_client import ApifyClient

# Initialize the ApifyClient with your Apify API token
# Replace '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = {
    "mode": "searchPackages",
    "searchQuery": "RNA-seq",
    "maxItems": 10,
}

# Run the Actor and wait for it to finish
run = client.actor("crawlerbros/bioconductor-scraper").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print(f"💾 Check your data here: https://console.apify.com/storage/datasets/{run.default_dataset_id}")
for item in client.dataset(run.default_dataset_id).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "mode": "searchPackages",
  "searchQuery": "RNA-seq",
  "maxItems": 10
}' |
apify call crawlerbros/bioconductor-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,crawlerbros/bioconductor-scraper"
        }
    }
}

```

The hosted server signs you in with OAuth on first connect, so no API token belongs in this config. Clients without OAuth support can send an `Authorization: Bearer <APIFY_API_TOKEN>` header instead, using a token from API & Integrations in Apify Console (https://console.apify.com/settings/integrations).

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/bucLdtXb9sZC7tMlZ/builds/bU0lruUzewVhfVKbC/openapi.json