# Bioconductor Package Metadata Scraper (`klondikeking/bioconductor-package-scraper`) Actor

Extract structured metadata from Bioconductor R package pages including version, license, dependencies, biocViews, and reverse dependencies.

- **URL**: https://apify.com/klondikeking/bioconductor-package-scraper.md
- **Developed by:** [Pierrick McD0nald](https://apify.com/klondikeking) (community)
- **Categories:** Developer tools, AI
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

$1.00 / 1,000 package extracteds

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.

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 Package Metadata Scraper — Extract R Package Details at Scale

The Bioconductor Package Metadata Scraper turns Bioconductor package detail pages into structured, machine-readable datasets. Point it at one or more package URLs and it returns clean metadata including version, license, dependencies, biocViews classification, and source repository links. Built for bioinformatics teams, R developers, and data vendors who need to track the Bioconductor ecosystem without manual copy-paste.

### Use Cases

- **Portfolio auditing** — Generate a complete inventory of packages, versions, and licenses across a Bioconductor installation or workflow.
- **Competitive research** — Compare dependency graphs, biocViews tags, and maintainer patterns across popular packages.
- **Data enrichment** — Add Bioconductor metadata to internal knowledge bases, catalogs, or recommendation engines.
- **Compliance & security** — Extract license and dependency information for open-source compliance reviews.

### Input

| Field | Type | Required | Description |
| --- | --- | --- | --- |
| `startUrls` | array | Yes | Bioconductor package detail page URLs, e.g. `https://www.bioconductor.org/packages/release/bioc/html/limma.html`. |
| `maxItems` | integer | No | Maximum packages to extract (default: `100`). |
| `includeReverseDependencies` | boolean | No | Include packages that depend on, import, suggest, or link to the scraped package (default: `false`). |
| `proxyConfiguration` | object | No | Proxy configuration. The built-in Apify proxy is used by default. |

### Output

The Actor outputs one dataset row per package with the following fields:

```json
{
  "sourceUrl": "https://www.bioconductor.org/packages/release/bioc/html/limma.html",
  "packageName": "limma",
  "title": "Linear Models for Microarray Data",
  "description": "Data analysis, linear models and differential expression for microarray data.",
  "version": "3.68.4",
  "inBioconductorSince": "BioC 1.6 (R-2.1) or earlier (> 21 years)",
  "license": "GPL (>=2)",
  "depends": "R (>= 3.6.0)",
  "imports": "grDevices, graphics, stats, utils, methods,statmod",
  "suggests": "BiasedUrn,ellipse,gplots,knitr,locfit,MASS, splines,affy,AnnotationDbi,Biobase",
  "systemRequirements": "",
  "homeUrl": "https://bioinf.wehi.edu.au/limma/",
  "biocViews": ["AlternativeSplicing", "BatchEffect", "Bayesian"],
  "sourcePackage": "limma_3.68.4.tar.gz",
  "sourceRepository": "git clone https://git.bioconductor.org/packages/limma",
  "packageShortUrl": "https://bioconductor.org/packages/limma/",
  "downloadsReportUrl": "Download Stats",
  "dependsOnMe": "",
  "importsMe": "",
  "suggestsMe": "",
  "linksToMe": ""
}
```

Note: reverse dependency fields are only populated when `includeReverseDependencies` is set to `true`.

### Pricing

Pay per event: **$0.001 per package extracted**. No monthly fees, no minimums. You are charged only for successful extractions.

### Limitations

- The Actor scrapes public Bioconductor package detail pages. It does not access private repositories or authenticated data.
- Page structure is tied to the current Bioconductor layout. Major site redesigns may require an update.
- Bioconductor pages are static HTML; no JavaScript rendering is required.

### FAQ

**Q: Can I scrape the entire Bioconductor repository?**\
A: Yes. Provide the package detail URLs you want to scrape and adjust `maxItems` accordingly. Be mindful of the target website's rate limits and your own usage budget.

**Q: Do I need a proxy?**\
A: The built-in Apify proxy is enabled by default. It can be disabled for small local tests, but we recommend keeping it enabled for production runs.

**Q: How do I report issues or request features?**\
A: Open an issue on this Actor's Apify page. Public support keeps response times visible and helps other users.

### Changelog

- **v1.0.10** — Refreshed build and validated cloud source. No source logic changes.
- **v1.0.9** — Refreshed build and validated cloud source. No source logic changes.
- **v1.0.8** — Refreshed build and validated cloud source. No source logic changes.
- **v1.0.7** — Refreshed build and validated cloud source. No source logic changes.
- **v1.0.6** — Refreshed build and validated cloud source. No source logic changes.
- **v1.0.5** — Refreshed build and validated cloud source. No source logic changes.
- **v1.0.2** — Refreshed build and hardened repository ignores. No source logic changes.
- **v1.0.0** — Initial release. Extracts package metadata, dependencies, and biocViews from Bioconductor package detail pages.

# Actor input Schema

## `startUrls` (type: `array`):

List of Bioconductor package detail page URLs (e.g. https://www.bioconductor.org/packages/release/bioc/html/limma.html).

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

Maximum number of packages to extract.

## `includeReverseDependencies` (type: `boolean`):

Include packages that depend on, import, suggest, or link to each scraped package.

## `proxyConfiguration` (type: `object`):

Proxy configuration used for scraping Bioconductor pages.

## Actor input object example

```json
{
  "startUrls": [
    "https://www.bioconductor.org/packages/release/bioc/html/limma.html"
  ],
  "maxItems": 10,
  "includeReverseDependencies": false,
  "proxyConfiguration": {
    "useApifyProxy": true
  }
}
```

# Actor output Schema

## `results` (type: `string`):

No description

## `stats` (type: `string`):

No description

# 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 = {
    "startUrls": [
        "https://www.bioconductor.org/packages/release/bioc/html/limma.html"
    ],
    "maxItems": 10,
    "proxyConfiguration": {
        "useApifyProxy": true
    }
};

// Run the Actor and wait for it to finish
const run = await client.actor("klondikeking/bioconductor-package-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 = {
    "startUrls": ["https://www.bioconductor.org/packages/release/bioc/html/limma.html"],
    "maxItems": 10,
    "proxyConfiguration": { "useApifyProxy": True },
}

# Run the Actor and wait for it to finish
run = client.actor("klondikeking/bioconductor-package-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 '{
  "startUrls": [
    "https://www.bioconductor.org/packages/release/bioc/html/limma.html"
  ],
  "maxItems": 10,
  "proxyConfiguration": {
    "useApifyProxy": true
  }
}' |
apify call klondikeking/bioconductor-package-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,klondikeking/bioconductor-package-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/O5QstyntCW4mwRGDh/builds/0hpoOj3VTgbufPtCZ/openapi.json