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Bioinformatik

Agent Skills für genomische Sequenzierungsanalyse, RNA-seq-Verarbeitung und computergestützte Biologieforschung durchsuchen.

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。

sparse-autoencoder-training

NousResearch/hermes-agent

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.

NousResearch/hermes-agent

Gateway to 400+ bioinformatics skills from bioSkills and ClawBio. Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, and more. Fetches domain-specific reference material on demand.

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.

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).

Vector search via embeddings_* (large-scale HNSW) and ruvllm_hnsw_* (WASM router for ≤11 hot patterns), with RaBitQ 1-bit quantization for 32× memory reduction

Detect and classify telemetry anomalies on Cognitum Seed devices

Pathfinder traversal of the knowledge graph starting from a seed entity

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.

sickn33/antigravity-awesome-skills

Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis.

skin-health-analyzer

sickn33/antigravity-awesome-skills

Analyze skin health data, identify skin problem patterns, assess skin health status. Supports correlation analysis with nutrition, chronic diseases, and medication data.

vector-database-engineer

sickn33/antigravity-awesome-skills

Expert in vector databases, embedding strategies, and semantic search implementation. Masters Pinecone, Weaviate, Qdrant, Milvus, and pgvector for RAG applications, recommendation systems, and similar

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

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.

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.

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

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

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.

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.

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

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

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 3.1 Pro Preview 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.

K-Dense-AI/scientific-agent-skills

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

assafelovic/gpt-researcher

Autonomous deep research from Codex via MCP

concept-synthesis

garrytan/gbrain

Deduplicate and synthesize raw concept stubs into a tiered intellectual map (T1 Canon to T4 Riff), tracing idea evolution across sources over time. Transforms thousands of raw concept pages into a curated intellectual fingerprint.

garrytan/gbrain

Trace one idea's evolution through the brain: first mention, best articulation, related concepts, reversals, contradictions, abandoned branches, and the current live version. Use for single-idea conceptual lineage, not broad concept-map synthesis or structured entity metrics.

nextflow-development

anthropics/knowledge-work-plugins

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.

single-cell-rna-qc

anthropics/knowledge-work-plugins

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.

analyzing-malware-family-relationships-with-malpedia

mukul975/Anthropic-Cybersecurity-Skills

Use the Malpedia platform and API to research malware family relationships, track variant evolution, link families to threat actors, and integrate YARA rules for detection across malware lineages.

analyzing-windows-lnk-files-for-artifacts

mukul975/Anthropic-Cybersecurity-Skills

Parse Windows LNK shortcut files to extract target paths, timestamps, volume information, and machine identifiers for forensic timeline reconstruction.

mapping-attack-paths-with-bloodhound-ce

mukul975/Anthropic-Cybersecurity-Skills

Collect Active Directory data with SharpHound and Entra ID data with AzureHound, ingest into BloodHound Community Edition, and analyze on-prem, cloud, and hybrid attack paths with built-in queries and custom Cypher.

audit-memory-retention

ben-manes/caffeine

Analyze reference retention paths that prevent GC of removed entries

danielmiessler/LifeOS

2-8 scientific lens passes to surface hidden requirements single-pass analysis misses. USE WHEN iterative depth, deep exploration, multi-angle analysis, multiple perspectives, examine from angles, surface hidden requirements.

biology-biopython

aiming-lab/AutoResearchClaw

Bioinformatics with Biopython for sequence manipulation, file parsing, BLAST, and phylogenetics. Use when working with DNA/RNA/protein sequences or biological databases.

aiming-lab/AutoResearchClaw

Analyse FBA flux distributions to extract biological insights. Covers gene essentiality, phenotypic phase planes, flux sampling, pathway-level aggregation, secretion product prediction, and production of publication- quality figures.

HKUDS/Vibe-Trading

Browse and bench the bundled alpha zoos — prebuilt cross-sectional factor libraries (Kakushadze 101, GTJA 191, Qlib 158, Fama-French / Carhart). Use when the user asks "which alphas exist", wants metadata on a named alpha, or wants to run IC/IR on a whole zoo over a universe.

Ingest a LeRobot (HuggingFace) dataset into Rerun. Read when converting a LeRobot dataset to RRDs, splitting it into per-episode segments, or registering it on a Rerun catalog. Covers the built-in directory importer (log_file_from_path), the RrdReader + send_chunks per-episode split, and when to drop to ParquetReader for custom control.

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