# Category: Search & Research | Category | Search & Research | | --- | --- | | Slug | search-research | | Count | 11 | --- stable_id: skills/knowledge-work-plugins-bio-research-skills-instrument-data-to-allotrope-skill type: skills title: instrument-data-to-allotrope summary: Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines. tags: - source-knowledge-work-plugins - plugin-bio-research - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/bio-research/skills/instrument-data-to-allotrope/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/bio-research/skills/instrument-data-to-allotrope/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:10:03.967Z content_sha256: 6167bf1731e568b63110a8f27e987cfe386f44e64cd2d78d9080d5d7628a79c5 --- |/data/knowledge-work-plugins-bio-research-skills-instrument-data-to-allotrope-skill| --- stable_id: skills/knowledge-work-plugins-bio-research-skills-nextflow-development-skill type: skills title: nextflow-development summary: Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation. tags: - source-knowledge-work-plugins - plugin-bio-research - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/bio-research/skills/nextflow-development/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/bio-research/skills/nextflow-development/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:10:04.012Z content_sha256: f30017df5d499427a701ec6cedfc5c9948ca3bd04ee1a2b6a585a29cd93ad0d7 --- |/data/knowledge-work-plugins-bio-research-skills-nextflow-development-skill| --- stable_id: skills/knowledge-work-plugins-bio-research-skills-scientific-problem-selection-skill type: skills title: scientific-problem-selection summary: This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research". tags: - source-knowledge-work-plugins - plugin-bio-research - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/bio-research/skills/scientific-problem-selection/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/bio-research/skills/scientific-problem-selection/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:10:04.191Z content_sha256: 9ec99e3e5b2f4cd7474ef2bb8a1b10ee1f97dbe688c7723c7ec0b18deb8ff0f4 --- |/data/knowledge-work-plugins-bio-research-skills-scientific-problem-selection-skill| --- stable_id: skills/knowledge-work-plugins-bio-research-skills-scvi-tools-skill type: skills title: scvi-tools summary: Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space. tags: - source-knowledge-work-plugins - plugin-bio-research - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/bio-research/skills/scvi-tools/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/bio-research/skills/scvi-tools/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:10:04.090Z content_sha256: 03a69b32b77db86afe5f87b75db2ae4c92b03b6e9e16e2c5e66cde2d4ad9c5bc --- |/data/knowledge-work-plugins-bio-research-skills-scvi-tools-skill| --- stable_id: skills/knowledge-work-plugins-bio-research-skills-single-cell-rna-qc-skill type: skills title: single-cell-rna-qc summary: Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis. tags: - source-knowledge-work-plugins - plugin-bio-research - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/bio-research/skills/single-cell-rna-qc/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/bio-research/skills/single-cell-rna-qc/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:10:04.138Z content_sha256: 49cb573916deec6fcf6cc2cb1b573469cbc8c34b84326597ce2db22d0202393f --- |/data/knowledge-work-plugins-bio-research-skills-single-cell-rna-qc-skill| --- stable_id: skills/knowledge-work-plugins-bio-research-skills-start-skill type: skills title: start summary: Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are connected, or surveying available analysis skills before starting a new project. tags: - source-knowledge-work-plugins - plugin-bio-research - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/bio-research/skills/start/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/bio-research/skills/start/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:11:05.258Z content_sha256: 6016fe5c28952feef14ac851134b35b56a1c86614d9163d21fb82205d7e7694b --- |/data/knowledge-work-plugins-bio-research-skills-start-skill| --- stable_id: skills/knowledge-work-plugins-enterprise-search-skills-digest-skill type: skills title: digest summary: Generate a daily or weekly digest of activity across all connected sources. Use when catching up after time away, starting the day and wanting a summary of mentions and action items, or reviewing a week's decisions and document updates grouped by project. tags: - source-knowledge-work-plugins - plugin-enterprise-search - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/enterprise-search/skills/digest/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/enterprise-search/skills/digest/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:11:07.350Z content_sha256: d711d49b898eb303b74488dce75308e8737786d87210f1dca13ec325bc7f5737 --- |/data/knowledge-work-plugins-enterprise-search-skills-digest-skill| --- stable_id: skills/knowledge-work-plugins-enterprise-search-skills-knowledge-synthesis-skill type: skills title: knowledge-synthesis summary: Combines search results from multiple sources into coherent, deduplicated answers with source attribution. Handles confidence scoring based on freshness and authority, and summarizes large result sets effectively. tags: - source-knowledge-work-plugins - plugin-enterprise-search - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/enterprise-search/skills/knowledge-synthesis/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/enterprise-search/skills/knowledge-synthesis/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:10:04.928Z content_sha256: 8dc66c66ef0004010bbf2d569251163e90a6675b982e0cb99ef26b4dd1c5a0f6 --- |/data/knowledge-work-plugins-enterprise-search-skills-knowledge-synthesis-skill| --- stable_id: skills/knowledge-work-plugins-enterprise-search-skills-search-skill type: skills title: search summary: Search across all connected sources in one query. Trigger with "find that doc about...", "what did we decide on...", "where was the conversation about...", or when looking for a decision, document, or discussion that could live in chat, email, cloud storage, or a project tracker. tags: - source-knowledge-work-plugins - plugin-enterprise-search - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/enterprise-search/skills/search/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/enterprise-search/skills/search/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:11:07.306Z content_sha256: 5330512ac1f71c4526a7cb8a072902053220a924db052fbace20d584d7cf1d52 --- |/data/knowledge-work-plugins-enterprise-search-skills-search-skill| --- stable_id: skills/knowledge-work-plugins-enterprise-search-skills-search-strategy-skill type: skills title: search-strategy summary: Query decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries into source-specific syntax, ranks results by relevance, and handles ambiguity and fallback strategies. tags: - source-knowledge-work-plugins - plugin-enterprise-search - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/enterprise-search/skills/search-strategy/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/enterprise-search/skills/search-strategy/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:10:04.997Z content_sha256: 71d5ba2d219a72d696e079885cba2fb5455ba5da6b1404491f8b945bdd8694c6 --- |/data/knowledge-work-plugins-enterprise-search-skills-search-strategy-skill| --- stable_id: skills/knowledge-work-plugins-enterprise-search-skills-source-management-skill type: skills title: source-management summary: Manages connected MCP sources for enterprise search. Detects available sources, guides users to connect new ones, handles source priority ordering, and manages rate limiting awareness. tags: - source-knowledge-work-plugins - plugin-enterprise-search - plugin-component-skills - plugin-skill - category-search-research source_url: https://raw.githubusercontent.com/anthropics/knowledge-work-plugins/main/enterprise-search/skills/source-management/SKILL.md license: "" upstream_ref: https://github.com/anthropics/knowledge-work-plugins/blob/main/enterprise-search/skills/source-management/SKILL.md github_stars: null github_forks: null github_is_organization: null retrieved_at: 2026-10-10T13:10:04.852Z content_sha256: 221d8acdc5c686033bb073d2bba83841892f6b8be0888c0267247fd1dd34461d --- |/data/knowledge-work-plugins-enterprise-search-skills-source-management-skill|