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バイオインフォマティクス - Agent Skills | SkillsMP
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bioinformatics
バイオインフォマティクス
ゲノムシーケンス解析、RNA-seq処理、計算生物学研究向けエージェントスキルを閲覧。
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nanoclaw-repl.md
165.9k
from
"affaan-m/everything-claude-code"
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。
2026-03-07
bioinformatics.md
114.8k
from
"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.
2026-03-21
smart-explore.md
66.8k
from
"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.
2026-04-10
scanpy.md
34.9k
from
"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.
2026-04-13
skin-health-analyzer.md
34.9k
from
"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.
2026-04-13
vector-database-engineer.md
34.9k
from
"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
2026-04-13
mma-investigator.md
32.1k
from
"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.
2026-03-02
neuropixels-analysis.md
25.1k
from
"davila7/claude-code-templates"
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
2025-12-20
gtars.md
19.3k
from
"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.
2026-03-03
anndata.md
19.3k
from
"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.
2026-03-03
arboreto.md
19.3k
from
"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.
2026-03-03
bioservices.md
19.3k
from
"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.
2026-03-03
cellxgene-census.md
19.3k
from
"K-Dense-AI/scientific-agent-skills"
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
2026-03-03
geniml.md
19.3k
from
"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.
2026-03-03
gget.md
19.3k
from
"K-Dense-AI/scientific-agent-skills"
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
2026-03-03
neuropixels-analysis.md
19.3k
from
"K-Dense-AI/scientific-agent-skills"
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
2026-04-11
phylogenetics.md
19.3k
from
"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.
2026-03-03
pydeseq2.md
19.3k
from
"K-Dense-AI/scientific-agent-skills"
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
2026-03-03
pysam.md
19.3k
from
"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.
2026-03-03
scanpy.md
19.3k
from
"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, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
2026-03-03
scientific-schematics.md
19.3k
from
"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.
2026-04-11
scikit-bio.md
19.3k
from
"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.
2026-03-03
scvelo.md
19.3k
from
"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.
2026-03-03
tiledbvcf.md
19.3k
from
"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.
2026-04-09
torchdrug.md
19.3k
from
"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.
2026-03-03
audit-memory-retention.md
17.6k
from
"ben-manes/caffeine"
Analyze reference retention paths that prevent GC of removed entries
2026-04-13
iterativedepth.md
11.7k
from
"danielmiessler/Personal_AI_Infrastructure"
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.
2026-02-28
biology-biopython.md
11.6k
from
"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.
2026-03-31
nextflow-development.md
11.5k
from
"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.
2026-03-18
single-cell-rna-qc.md
11.5k
from
"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.
2026-01-29
sparse-autoencoder-training.md
7.3k
from
"Orchestra-Research/AI-Research-SKILLs"
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.
2025-12-17
kernel-analysis-vphone600.md
5.7k
from
"Lakr233/vphone-cli"
Analyze vphone600 kernel artifacts using the local symbol database and XNU source tree. Use when working on kernel reverse engineering, address-to-symbol lookup, release-vs-research kernel comparison, or patch analysis for vphone600 variants in this repository.
2026-03-05
analyzing-malware-family-relationships-with-malpedia.md
5.7k
from
"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.
2026-04-06
analyzing-windows-lnk-files-for-artifacts.md
5.7k
from
"mukul975/Anthropic-Cybersecurity-Skills"
Parse Windows LNK shortcut files to extract target paths, timestamps, volume information, and machine identifiers for forensic timeline reconstruction.
2026-04-06
trailmark-structural.md
4.8k
from
"trailofbits/skills"
Runs full trailmark structural analysis with all pre-analysis passes (blast radius, taint propagation, privilege boundaries, complexity hotspots). Use when vivisect needs detailed structural data for a target. Triggers: structural analysis, blast radius, taint analysis, complexity hotspots.
2026-03-31
cognitive-agent.md
4.3k
from
"openclaw/skills"
基于认知天性理论的类人 AI 生命体框架，让 AI 具备人类学习、记忆、成长的特性
2026-03-21
memory-system-complete.md
4.3k
from
"openclaw/skills"
Complete memory system with causal graph, knowledge graph, auto-detection, and evolution features
2026-04-14
med-critical-disease-review.md
4.3k
from
"openclaw/skills"
重大疾病理赔智能评估（支持 28 种病种）。输入住院病历结构化数据，调用内网评估接口，输出原始 JSON 与自然语言结论（结论 + 证据）。
2026-03-25
aavegotchi-traits.md
4.3k
from
"openclaw/skills"
Retrieve Aavegotchi NFT data by gotchi ID or name on Base. Returns traits, wearables, rarity scores, kinship, XP, level, and owner data.
2026-03-07
fluid-memory.md
4.3k
from
"openclaw/skills"
基于艾宾浩斯遗忘曲线和访问频率的衰减模型设计的遗忘和归档机制，完全依赖openclaw原生记忆系统的拟人化流体记忆系统
2026-03-06
dna.md
4.3k
from
"openclaw/skills"
Biological code execution and genomic intelligence system. Translates raw A-T-C-G sequences into actionable health, longevity, and pharmacogenomic protocols. The bridge between your biological identity and your agent's decision-making engine.
2026-03-09
antibody-humanizer.md
4.3k
from
"openclaw/skills"
Humanize murine antibody sequences using CDR grafting and framework optimization to reduce immunogenicity while preserving antigen binding. Predicts optimal human germline frameworks and identifies critical back-mutations for therapeutic antibody development.
2026-03-18
bio-ontology-mapper.md
4.3k
from
"openclaw/skills"
Map unstructured biomedical text to standardized ontologies (SNOMED CT.
2026-04-02
cnv-caller-plotter.md
4.3k
from
"openclaw/skills"
Detect copy number variations from whole genome sequencing data and generate publication-quality genome-wide CNV plots. Supports CNV calling, segmentation, and visualization for cancer genomics and rare disease analysis.
2026-03-18
cold-chain-risk-calculator.md
4.3k
from
"openclaw/skills"
Calculate cold chain transport risks
2026-03-18
crispr-grna-designer.md
4.3k
from
"openclaw/skills"
Design CRISPR gRNA sequences for specific gene exons with off-target prediction and efficiency scoring. Trigger when user needs gRNA design, CRISPR guide RNA selection, or genome editing target analysis.
2026-03-18
dual-disease-transcriptomic-ml-planner.md
4.3k
from
"openclaw/skills"
Generates complete dual-disease transcriptomic + machine learning research designs from a user-provided disease pair. Use when users want to identify shared DEGs, common hub genes, cross-disease biomarkers, or shared molecular mechanisms between two diseases using public GEO data. Triggers: "shared biomarker study for two diseases", "dual-disease transcriptomic ML paper", "identify common DEGs between disease A and B", "cross-disease hub gene discovery", "shared DEG + PPI + ROC design", "immune infiltration shared biomarker", or "I want to study disease X and Y together". Always outputs four workload configurations (Lite / Standard / Advanced / Publication+) with a recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, and publication upgrade path.
2026-03-14
fastqc-report-interpreter.md
4.3k
from
"openclaw/skills"
Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.
2026-03-21
