# 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 Pay per usage This Actor is paid per platform usage. The Actor is free to use, and you only pay for the Apify platform usage, which gets cheaper the higher subscription plan you have. Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-usage ## What's an Apify Actor? Actors are a software tools running on the Apify platform, for all kinds of web data extraction and automation use cases. 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. In JavaScript/TypeScript projects, use official [JavaScript/TypeScript client](https://docs.apify.com/api/client/js.md): ```bash npm install apify-client ``` In Python projects, use official [Python client library](https://docs.apify.com/api/client/python.md): ```bash pip install apify-client ``` In shell scripts, use [Apify CLI](https://docs.apify.com/cli/docs.md): ````bash # MacOS / Linux curl -fsSL https://apify.com/install-cli.sh | bash # Windows irm https://apify.com/install-cli.ps1 | iex ```bash In AI frameworks, you might use the [Apify MCP server](https://docs.apify.com/platform/integrations/mcp.md). If your project is in a different language, use 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 - **v1.0.0** — 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 '' with your token const client = new ApifyClient({ 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 '' with your token. client = ApifyClient("") # 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("💾 Check your data here: https://console.apify.com/storage/datasets/" + run["defaultDatasetId"]) for item in client.dataset(run["defaultDatasetId"]).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": { "command": "npx", "args": [ "mcp-remote", "https://mcp.apify.com/?tools=klondikeking/bioconductor-package-scraper", "--header", "Authorization: Bearer " ] } } } ``` ## OpenAPI specification ```json { "openapi": "3.0.1", "info": { "title": "Bioconductor Package Metadata Scraper", "description": "Extract structured metadata from Bioconductor R package pages including version, license, dependencies, biocViews, and reverse dependencies.", "version": "1.0", "x-build-id": "xgLEcNrGiKE6hAVGZ" }, "servers": [ { "url": "https://api.apify.com/v2" } ], "paths": { "/acts/klondikeking~bioconductor-package-scraper/run-sync-get-dataset-items": { "post": { "operationId": "run-sync-get-dataset-items-klondikeking-bioconductor-package-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for its completion, and returns Actor's dataset items in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } }, "/acts/klondikeking~bioconductor-package-scraper/runs": { "post": { "operationId": "runs-sync-klondikeking-bioconductor-package-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor and returns information about the initiated run in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/runsResponseSchema" } } } } } } }, "/acts/klondikeking~bioconductor-package-scraper/run-sync": { "post": { "operationId": "run-sync-klondikeking-bioconductor-package-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } } }, "components": { "schemas": { "inputSchema": { "type": "object", "required": [ "startUrls" ], "properties": { "startUrls": { "title": "Bioconductor package URLs", "type": "array", "description": "List of Bioconductor package detail page URLs (e.g. https://www.bioconductor.org/packages/release/bioc/html/limma.html).", "items": { "type": "string" } }, "maxItems": { "title": "Max items", "type": "integer", "description": "Maximum number of packages to extract.", "default": 100 }, "includeReverseDependencies": { "title": "Include reverse dependencies", "type": "boolean", "description": "Include packages that depend on, import, suggest, or link to each scraped package.", "default": false }, "proxyConfiguration": { "title": "Proxy Configuration", "type": "object", "description": "Proxy configuration used for scraping Bioconductor pages." } } }, "runsResponseSchema": { "type": "object", "properties": { "data": { "type": "object", "properties": { "id": { "type": "string" }, "actId": { "type": "string" }, "userId": { "type": "string" }, "startedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "finishedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "status": { "type": "string", "example": "READY" }, "meta": { "type": "object", "properties": { "origin": { "type": "string", "example": "API" }, "userAgent": { "type": "string" } } }, "stats": { "type": "object", "properties": { "inputBodyLen": { "type": "integer", "example": 2000 }, "rebootCount": { "type": "integer", "example": 0 }, "restartCount": { "type": "integer", "example": 0 }, "resurrectCount": { "type": "integer", "example": 0 }, "computeUnits": { "type": "integer", "example": 0 } } }, "options": { "type": "object", "properties": { "build": { "type": "string", "example": "latest" }, "timeoutSecs": { "type": "integer", "example": 300 }, "memoryMbytes": { "type": "integer", "example": 1024 }, "diskMbytes": { "type": "integer", "example": 2048 } } }, "buildId": { "type": "string" }, "defaultKeyValueStoreId": { "type": "string" }, "defaultDatasetId": { "type": "string" }, "defaultRequestQueueId": { "type": "string" }, "buildNumber": { "type": "string", "example": "1.0.0" }, "containerUrl": { "type": "string" }, "usage": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "integer", "example": 1 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } }, "usageTotalUsd": { "type": "number", "example": 0.00005 }, "usageUsd": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "number", "example": 0.00005 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } } } } } } } } } ```