Research

Metabolomics pathway analysis using MetaboAnalystR (KEGG, Reactome), pathview visualization, MSEA, mummichog, and network-based topology analysis.

Parse scientific literature (PDFs, URLs, DOIs) to extract GEO accessions, metadata, and datasets. Use when users provide a paper and want to automatically extract data sources for downstream omics analysis.

Germline and somatic variant calling (SNVs, Indels) using GATK HaplotypeCaller, Mutect2, DeepVariant, or FreeBayes. Includes GVCF workflow, VQSR, and hard filtering.

Epigenomics analysis including ATAC-seq peak calling with MACS3, ChIP-seq analysis, motif enrichment, and chromatin accessibility.

Copy number variant detection from exome/WGS data using CNVkit, Control-FREEC, or GATK gCNV. Supports tumor-normal pairs, tumor-only, and germline modes.

Gene identifier conversion between Ensembl, Entrez, HGNC symbols, and UniProt for bulk RNA-seq count matrices.

--> --- name: bio-biomedical-rag-citation-pipelines description: Design citation-grounded biomedical retrieval and generation systems for literature-heavy assistants. Use when building or improving PubMed or PMC search pipelines, hybrid retrieval, claim-to-citation validation, evidence-aware answer synthesis, or evaluation workflows for biomedical RAG applications. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minute...

--> --- name: bio-bulkrna-alignment description: "Bulk RNA-seq count matrix QC \u2014 library size, gene detection rates,\ \ and sample correlation." tool_type: mixed primary_tool: bulkrna measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Library size distribution, gene detection rates, and sample correlation analysis for bulk RNA-seq count matrices.

--> --- name: bio-spatial-enrichment description: Pathway and gene set enrichment analysis for spatial transcriptomics data. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Enrichment**, a specialised OmicsClaw agent for pathway and gene set enrichment analysis. Your role is to identify over-represented biological pathways in spatially resolv...

--> --- name: bio-spatial-condition description: Experimental condition comparison using pseudobulk differential expression with proper multi-sample statistics. tool_type: mixed primary_tool: spatial measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **Spatial Condition**, a specialised OmicsClaw agent for comparing experimental conditions in spatial transcriptomics data. Your role is to perfo...

--> --- name: codebase-investigator description: Expertly analyze large codebases to identify patterns, dependencies, and architectural flaws. keywords: - refactoring - analysis - architecture - discovery - search measurable_outcome: Map key components and data flows of a 50k+ LOC repo within 5 minutes, identifying 3+ potential improvements. license: MIT metadata: author: AI Agentic Skills Team version: "2.0.0" compatibility: - system: linux, macos allowed-tools: - list_directory - read_file ...

--> --- name: bio-paperzilla description: Reads content from URLs or files, classifies it, and generates structured summaries and comments in a specific, analytical style. Optimized for deep biomedical paper review. tool_type: mixed primary_tool: read_file measurable_outcome: Generate a structured analytical review of a biomedical paper with 100% citation accuracy. allowed-tools: - read_file - run_shell_command --- You are **Paperzilla**, an expert biomedical analyst. Your goal is to process ...

--> --- name: bio-biomed-dispatch description: 'Dispatch biomedical research and data analysis tasks to Claude Code with K-Dense Scientific Skills. Use this skill when the user asks to run any bioinformatics, genomics, drug discovery, clinical data analysis, proteomics, multi-omics, medical imaging, or scientific computation task. Also use for literature search (PubMed, bioRxiv), pathway analysis, protein structure prediction, or scientific writing tasks. ' tool_type: mixed primary_tool: Unkn...

--> --- name: bio-zinc-database description: Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-what-if-oracle description: Run structured What-If scenario analysis with multi-branch possibility exploration. Use this skill when the user asks speculative questions like "what if...", "what would happen if...", "what are the possibilities", "explore scenarios", "scenario analysis", "possibility space", "what could go wrong", "best case / worst case", "risk analysis", "contingency planning", "strategic options", or any question about uncertain futures. Also trigger when th...

--> --- name: bio-venue-templates description: Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requir...

--> --- name: bio-treatment-plans description: Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actiona...

--> --- name: bio-string-database description: Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-statistical-analysis description: Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 ...

--> --- name: bio-scientific-writing description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions. tool_type: mixed primary_tool: Unknown measurable...

--> --- name: bio-scientific-slides description: Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output with...

--> --- name: bio-scientific-critical-thinking description: Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully w...

--> --- name: bio-scientific-brainstorming description: Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully wit...

--> --- name: bio-scholar-evaluation description: Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---