生物信息学

浏览基因组测序分析、RNA-seq 处理和计算生物学研究的 agent skills。

healthcare-emr-patterns

電子医療記録（EMR）パターン、相互運用性、およびHL7/FHIR統合。

操作并扩展NanoClaw v2，这是ECC基于claude -p构建的零依赖会话感知REPL。

NousResearch/hermes-agent

Structured LLM outputs validated with Pydantic.

NousResearch/hermes-agent

Gateway to 400+ genomics and computational biology skills.

NousResearch/hermes-agent

llama.cpp local GGUF inference + HF Hub model discovery.

n8n-conventions

Quick reference for n8n patterns. Full docs /AGENTS.md

thedotmack/claude-mem

Token-optimized structural code search using tree-sitter AST parsing. Use instead of reading full files when you need to understand code structure, find functions, or explore a codebase efficiently.

Pathfinder traversal of the knowledge graph starting from a seed entity

Detect and classify candlestick patterns from ingested OHLCV data

7-section repo readiness report from `metaharness genome <path>`. Returns repo_type / agent_topology / risk_score / mcp_surface / test_confidence / publish_readiness. Pure-read; degrades gracefully (ADR-150).

Run a GEPA learning cycle via `metaharness learn` (upstream ADR-235, metaharness@0.3.0) — optimizes a harness genome against a SWE-bench-style slice manifest. $0 dry-run by default; `--run` is the explicit spend opt-in. Requires a metaharness repo checkout (`--repo` or $METAHARNESS_REPO) — without one it reports `checkout-required` with clone instructions. Degrades gracefully when metaharness is absent.

harness-similarity

ADR-152 — weighted similarity between two harness fingerprints (genome + score JSON). Returns overall score in [0,1] plus per-component breakdown (cosine over 9 numerics, categorical agreement over 4 enums, jaccard over agent_topology). Unblocks ADR-151 §3.2 Recommender, §3.3 Drift Detection, §3.5 Plugin Compat. Pure-TS, no `@metaharness/*` dep — preserves ADR-150's four architectural constraints.

mma-investigator

cockroachdb/cockroach

Expert system for investigating MMA (Multi-Metric Allocator) behavior on CockroachDB clusters. Helps oncall engineers diagnose load imbalances, understand rebalancing decisions, and identify why MMA did or didn't act.

K-Dense-AI/scientific-agent-skills

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

K-Dense-AI/scientific-agent-skills

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

K-Dense-AI/scientific-agent-skills

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

K-Dense-AI/scientific-agent-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.

cellxgene-census

K-Dense-AI/scientific-agent-skills

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.

dnanexus-integration

K-Dense-AI/scientific-agent-skills

Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.

K-Dense-AI/scientific-agent-skills

Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.

K-Dense-AI/scientific-agent-skills

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.

genomic-intelligence

K-Dense-AI/scientific-agent-skills

Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights. Six tasks over a REST API and a hosted MCP server (keyless public demo): promoter regions, splice donor/acceptor sites, enhancer activity, chromatin state, sequence-to-expression (log TPM), and de-novo gene annotation, plus a composite find-genes-then-predict-expression workflow. Use when the user has a gene symbol, a genomic region, or a DNA/FASTA sequence and wants any of these predictions, mentions Genomic Intelligence, genomicintelligence.ai, api.genomicintelligence.ai, or mcp.genomicintelligence.ai.

K-Dense-AI/scientific-agent-skills

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

K-Dense-AI/scientific-agent-skills

Use Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and the CLI.

neuropixels-analysis

K-Dense-AI/scientific-agent-skills

Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). Use when working with Neuropixels 1.0/2.0 recordings, spike sorting, or extracellular electrophysiology analysis.

K-Dense-AI/scientific-agent-skills

Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individuals. Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations.

pathway-enrichment

K-Dense-AI/scientific-agent-skills

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".

K-Dense-AI/scientific-agent-skills

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

K-Dense-AI/scientific-agent-skills

Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.

K-Dense-AI/scientific-agent-skills

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

scientific-schematics

K-Dense-AI/scientific-agent-skills

Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

K-Dense-AI/scientific-agent-skills

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

K-Dense-AI/scientific-agent-skills

RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.

K-Dense-AI/scientific-agent-skills

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.

sparse-autoencoder-training

davila7/claude-code-templates

Provides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.

rag-implementation

davila7/claude-code-templates

Retrieval-Augmented Generation patterns including chunking, embeddings, vector stores, and retrieval optimization Use when: rag, retrieval augmented, vector search, embeddings, semantic search.

alphafold-database

davila7/claude-code-templates

Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

davila7/claude-code-templates

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

davila7/claude-code-templates

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

brenda-database

davila7/claude-code-templates

Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

cellxgene-census

davila7/claude-code-templates

Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.

clinpgx-database

davila7/claude-code-templates

Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.

clinvar-database

davila7/claude-code-templates

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

ensembl-database

davila7/claude-code-templates

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

davila7/claude-code-templates

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

davila7/claude-code-templates

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

davila7/claude-code-templates

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

davila7/claude-code-templates

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.