All Skills

End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g. "analyze my RNA-seq", "FASTQ to DESeq2", "run nf-core/rnaseq", "STAR/Salmon quantification", "build a counts matrix for DESeq2", or "go from reads to differentially expressed genes and enriched pathways". Routes between an nf-core/rnaseq (Nextflow) path and a standalone STAR/Salmon path, and covers experimental design, strandedness, and QC gates. For single-cell RNA-seq use the scanpy skill instead.

Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.

Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++, Java, Go, Rust) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modeling, marine spatial analysis, atmospheric science, and any geospatial computation task.

Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation with Bionty, collections, branches, storage, and workflow integrations.

Search and read full-text biomedical papers, FDA/PMDA/EMA regulatory documents, clinical trial registries, and UniProt/PDB/ChEMBL entries with the Paperclip CLI from GXL. Covers installing and authenticating the `paperclip` binary with a PAPERCLIP_API_KEY, the read-only virtual filesystem under /papers, /fda, /trials, /proteins and /clipboard, source-scoped semantic search, corpus-wide grep, metadata lookup and SQL, map/reduce reading across many papers, figure vision analysis, opt-in paper repositories with claim verification, and line-pinned citations. Use when asked to install paperclip, run paperclip search/grep/map/reduce/sql/repo, find or read biomedical literature, regulatory filings or clinical trials through paperclip, or produce citations with line numbers.

Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.

Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance. Do not use for inference, ranking, open-ended pathfinding, clinical guidance, or sensitive queries.

Create, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks (random, scale-free, small-world), reading/writing graph file formats, or drawing network topologies. Common applications include social, biological, transportation, and citation networks.

Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

Search 11 academic literature APIs for papers, preprints, citations, and open-access full text, and return results with reproducible provenance. Covers PubMed, PMC (full text), Europe PMC (full-text and preprint search), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall. Use when searching for papers, citations, DOI/PMID/arXiv lookups, abstracts, full text, open-access PDFs, preprints, citation graphs, author publications, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X", "look up this DOI", "who cites this paper", or "get me the PDF".

Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".

Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design.

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.

Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready analysis plans. Use when turning observations or preliminary findings into transparent, testable research plans without treating hypotheses as facts.

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.

High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-core processing, Arrow interoperability, and optional GPU execution.

Check Web API and CSS feature compatibility in WebF - determine what JavaScript APIs, DOM methods, CSS properties, and layout modes are supported. Use when planning features, debugging why APIs don't work, or finding alternatives for unsupported features like IndexedDB, WebGL, float layout, or CSS Grid.

Skill for using the KnowledgeIndex registry to discover which directories contain `.knowledge.yaml` files without walking the filesystem. KnowledgeIndex is a lightweight SQLite cache. It maps directory paths to file metadata (mtime, memory_count, link_count). The database path is caller-provided — npcpy does not hardcode a default. Key operations: - Upsert a directory after writing to its YAML: `upsert_directory(db_path, directory, memory_count, link_count)` - List known directories: `get_known_directories(db_path, min_mtime=None)` - Full rescan of a tree: `scan_root(db_path, root, max_depth=5)` - Remove a stale directory: `remove_directory(db_path, directory)` Typical flow: 1. Call `scan_root(db_path, root="/home/user/projects", max_depth=5)` to populate the index with every `.knowledge.yaml` found. 2. Query `get_known_directories(db_path)` to get a list of directories with memory/link counts. 3. For each directory of interest, instantiate `KnowledgeStore(directory)` and call `load()` or `build_context()`. The index is a cache, not the source of truth. If a `.knowledge.yaml` is deleted or modified outside the app, re-run `scan_root` to refresh.

Skill for searching and evolving the SQLite-backed Knowledge Graph. Use this when you need structured fact/concept/link search across one or more teams, NPCs, or directory scopes. The Knowledge Graph (KG) is stored in the application's database (not YAML). It is scoped by (team_name, npc_name, directory_path). Facts and concepts carry generation numbers and origin tags. Search methods (choose the right one): 1. Keyword search — fast substring match over fact statements. `kg_search_facts(engine_or_kg, "keyword")` → List[str] 2. Embedding search — semantic cosine similarity via vector embeddings. `kg_embedding_search(engine_or_kg, query="...", embedding_model="nomic-embed-text", embedding_provider="ollama", similarity_threshold=0.6, max_results=20)` → List[dict] with 'content', 'type', 'score' 3. Link search — graph traversal (BFS/DFS) starting from keyword-matched seeds. `kg_link_search(engine_or_kg, query="...", max_depth=2, breadth_per_step=5, strategy="bfs", max_results=20)` → List[dict] with 'content', 'type', 'depth', 'path', 'score' 4. Hybrid search — combines keyword + embedding + link, boosting results found by multiple methods. `kg_hybrid_search(engine_or_kg, query="...", mode="all", max_depth=2, similarity_threshold=0.6, max_results=20)` → List[dict] with 'content', 'type', 'score', 'source' Graph evolution (use sparingly, usually in background): - `kg_initial(content, model, provider)` — build a new KG from text - `kg_evolve_incremental(existing_kg, new_content_text, ...)` — add content - `kg_sleep_process(existing_kg, model, provider)` — prune/deepen/consolidate - `kg_dream_process(existing_kg, model, provider, num_seeds)` — speculative synthesis When a user asks a question that spans facts, concepts, and their relationships, prefer hybrid search. For pure semantic similarity without graph structure, use embedding search. For exploring connected neighborhoods, use link search with BFS.

Skill for working with local .knowledge.yaml files via KnowledgeStore. Use this when you need to recall, search, or manage directory-local memories and knowledge links stored in plain YAML alongside the user's project files. KnowledgeStore is directory-scoped. Each directory that contains a `.knowledge.yaml` file maintains its own append-only memory graph. There is no global database — the YAML IS the source of truth. Key operations: - Load a directory's store: `npcpy.memory.knowledge_store.get_store_for_path(path)` - Append a memory: `store.append_memory(initial_memory="...", status="pending_approval", ...)` - Update a memory (approve/reject/edit): `store.update_memory(mem_id, status, final_memory)` - Search memories (keyword substring): `store.search_memories("query", limit=20)` - Get approved context for LLM prompts: `store.build_context(max_memories=10)` - Get links for a memory: `store.get_links_for_memory(mem_id)` - Create a link between memories: `store.append_link(from_mem, to_mem, relation="refines", agent="your_name")` - Aggregate across a tree: `KnowledgeStore.aggregate(root_directory, max_depth=3)` Memory statuses: - `pending_approval` — raw extraction, needs human review - `human-approved` — confirmed and available for context injection - `human-rejected` — discard, can be used as negative examples - `human-edited` — corrected version supersedes initial_memory When answering questions, prefer `build_context()` for recently approved local knowledge, and `search_memories()` for targeted recall. Always respect `human-rejected` memories — do not repeat them.

WordPress performance code review and optimization analysis. Use when reviewing WordPress PHP code for performance issues, auditing themes/plugins for scalability, optimizing WP_Query, analyzing caching strategies, checking code before launch, or detecting anti-patterns, or when user mentions "performance review", "optimization audit", "slow WordPress", "slow queries", "high-traffic", "scale WordPress", "code review", "timeout", "500 error", "out of memory", or "site won't load". Detects anti-patterns in database queries, hooks, object caching, AJAX, and template loading.