# 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: 2026-06-11T08:31:57.925Z
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: 2026-06-11T08:31:57.989Z
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: 2026-06-11T08:31:58.127Z
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: 2026-06-11T08:31:58.040Z
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: 2026-06-11T08:31:58.082Z
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: 2026-06-11T08:32:48.026Z
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: 2026-06-11T08:32:52.580Z
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: 2026-06-11T08:31:59.286Z
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: 2026-06-11T08:32:52.533Z
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: 2026-06-11T08:31:59.346Z
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: 2026-06-11T08:31:59.233Z
content_sha256: 221d8acdc5c686033bb073d2bba83841892f6b8be0888c0267247fd1dd34461d
---
|/data/knowledge-work-plugins-enterprise-search-skills-source-management-skill|
