FreedomIntelligence/OpenClaw-Medical-Skills

这个仓库里有 897 个技能，GitHub 星标 ★ 3,010。

• aav-vector-design-agent
• adaptyvCloud laboratory platform for automated protein testing and validation. Use when
• adhd-daily-plannerTime-blind friendly planning, executive function support, and daily structure fo
• aeonThis skill should be used for time series machine learning tasks including class
• agent-browserBrowse the web for any task — research topics, read articles, interact with web
• agentd-drug-discovery
• ai-analyzerAI驱动的综合健康分析系统，整合多维度健康数据、识别异常模式、预测健康风险、提供个性化建议。支持智能问答和AI健康报告生成。
• alphafold>
• alphafold-databaseAccess AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by
• anndataThis skill should be used when working with annotated data matrices in Python, p
• MAGE
• antibody-design-agent
• arboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable a
• armored-cart-design-agent
• arxiv-searchSearch arXiv physics, math, and computer science preprints using natural languag
• autonomous-oncology-agent
• bayesian-optimizer
• benchling-integrationBenchling R&D platform integration. Access registry (DNA, proteins), inventory,
• bgpt-paper-searchSearch scientific papers and retrieve structured experimental data extracted fro
• bindcraft>
• binder-design>
• binding-characterization>
• bindingdb-databaseQuery BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50)
• bio-admet-predictionPredicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates b
• bio-alignment-files-bam-statistics
• bio-alignment-filtering
• bio-alignment-indexing
• bio-alignment-ioRead, write, and convert multiple sequence alignment files using Biopython Bio.A
• bio-alignment-msa-parsingParse and analyze multiple sequence alignments using Biopython. Extract sequence
• bio-alignment-msa-statisticsCalculate alignment statistics including sequence identity, conservation scores,
• bio-alignment-pairwisePerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. U
• bio-alignment-sorting
• bio-alignment-validation
• bio-atac-seq-atac-peak-callingCall accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-speci
• bio-atac-seq-atac-qcQuality control metrics for ATAC-seq data including fragment size distribution,
• bio-atac-seq-differential-accessibilityFind differentially accessible chromatin regions between conditions using DiffBi
• bio-atac-seq-footprintingDetect transcription factor binding sites through footprinting analysis in ATAC-
• bio-atac-seq-motif-deviationAnalyze transcription factor motif accessibility variability using chromVAR. Use
• bio-atac-seq-nucleosome-positioningExtract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and
• bio-basecallingConvert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dora
• bio-batch-downloads
• bio-batch-processingProcess multiple sequence files in batch using Biopython. Use when working with
• bio-bedgraph-handling
• bio-blast-searches
• bio-causal-genomics-colocalization-analysisTest whether two traits share a causal variant at a genomic locus using Bayesian
• bio-causal-genomics-fine-mappingIdentify likely causal variants within GWAS loci using SuSiE for sum of single e
• bio-causal-genomics-mediation-analysisDecompose genetic effects into direct and indirect paths through mediating varia
• bio-causal-genomics-mendelian-randomizationEstimate causal effects between exposures and outcomes using genetic variants as
• bio-causal-genomics-pleiotropy-detectionDetect and correct for horizontal pleiotropy in Mendelian randomization analyses
• bio-cfdna-preprocessingPreprocesses cell-free DNA sequencing data including adapter trimming, alignment
• bio-chipseq-differential-bindingDifferential binding analysis using DiffBind. Compare ChIP-seq peaks between con
• bio-chipseq-motif-analysisDe novo motif discovery and known motif enrichment analysis using HOMER and MEME
• bio-chipseq-peak-annotationAnnotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign p
• bio-chipseq-peak-callingChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcriptio
• bio-chipseq-qcChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cr
• bio-chipseq-super-enhancersIdentifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related too
• bio-chipseq-visualizationVisualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps,
• bio-clinical-databases-clinvar-lookupQuery ClinVar for variant pathogenicity classifications, review status, and dise
• bio-clinical-databases-dbsnp-queriesQuery dbSNP for rsID lookups, variant annotations, and cross-references to other
• bio-clinical-databases-gnomad-frequenciesQuery gnomAD for population allele frequencies to assess variant rarity. Use whe
• bio-clinical-databases-hla-typingCall HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogen
• bio-clinical-databases-myvariant-queriesQuery myvariant.info API for aggregated variant annotations from multiple databa
• bio-clinical-databases-pharmacogenomicsQuery PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations,
• bio-clinical-databases-polygenic-riskCalculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS sum
• bio-clinical-databases-somatic-signaturesExtract and analyze mutational signatures from somatic variants using SigProfile
• bio-clinical-databases-tumor-mutational-burdenCalculate tumor mutational burden from panel or WES data with proper normalizati
• bio-clinical-databases-variant-prioritizationFilter and prioritize variants by pathogenicity, population frequency, and clini
• bio-clip-seq-binding-site-annotation
• bio-clip-seq-clip-alignment
• bio-clip-seq-clip-motif-analysis
• bio-clip-seq-clip-peak-calling
• bio-clip-seq-clip-preprocessing
• bio-codon-usage
• bio-comparative-genomics-ancestral-reconstruction
• bio-comparative-genomics-hgt-detection
• bio-comparative-genomics-ortholog-inference
• bio-comparative-genomics-positive-selection
• bio-comparative-genomics-synteny-analysis
• bio-compressed-filesRead and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Us
• bio-consensus-sequencesGenerate consensus FASTA sequences by applying VCF variants to a reference using
• bio-copy-number-cnv-annotationAnnotate CNVs with genes, pathways, and clinical significance. Use when interpre
• bio-copy-number-cnv-visualizationVisualize copy number profiles, segments, and compare across samples. Create pub
• bio-copy-number-cnvkit-analysisDetect copy number variants from targeted/exome sequencing using CNVkit. Support
• bio-copy-number-gatk-cnvCall copy number variants using GATK best practices workflow. Supports both soma
• bio-crispr-screens-base-editing-analysisAnalyzes base editing and prime editing outcomes including editing efficiency, b
• bio-crispr-screens-batch-correctionBatch effect correction for CRISPR screens. Covers normalization across batches,
• bio-crispr-screens-crispresso-editingCRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR e
• bio-crispr-screens-hit-callingStatistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, d
• bio-crispr-screens-jacks-analysisJACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA effica
• bio-crispr-screens-library-designCRISPR library design for genetic screens. Covers sgRNA selection, library compo
• bio-crispr-screens-mageck-analysisMAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRI
• bio-crispr-screens-screen-qcQuality control for pooled CRISPR screens. Covers library representation, read d
• bio-ctdna-mutation-detectionDetects somatic mutations in circulating tumor DNA using variant callers optimiz
• bio-data-visualization-circos-plots
• bio-data-visualization-color-palettes
• bio-data-visualization-genome-browser-tracks
• bio-data-visualization-genome-tracks
• bio-data-visualization-ggplot2-fundamentals
• bio-data-visualization-heatmaps-clustering
• bio-data-visualization-interactive-visualization
• bio-data-visualization-multipanel-figures
• bio-data-visualization-specialized-omics-plots
• bio-data-visualization-upset-plots
• bio-data-visualization-volcano-customization
• bio-de-deseq2-basicsPerform differential expression analysis using DESeq2 in R/Bioconductor. Use for
• bio-de-edger-basicsPerform differential expression analysis using edgeR in R/Bioconductor. Use for
• bio-de-resultsExtract, filter, annotate, and export differential expression results from DESeq
• bio-de-visualizationVisualize differential expression results using DESeq2/edgeR built-in functions.
• bio-differential-expression-batch-correctionRemove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBat
• bio-differential-expression-timeseries-deAnalyze time-series RNA-seq data using limma voom with splines, maSigPro, and Im
• bio-differential-splicingDetects differential alternative splicing between conditions using rMATS-turbo (
• bio-duplicate-handling
• bio-entrez-fetch
• bio-entrez-link
• bio-entrez-search
• bio-epidemiological-genomics-amr-surveillanceDetect and track antimicrobial resistance genes using AMRFinderPlus and ResFinde
• bio-epidemiological-genomics-pathogen-typingPerform multi-locus sequence typing (MLST), core genome MLST, and SNP-based stra
• bio-epidemiological-genomics-phylodynamicsConstruct time-scaled phylogenies and infer evolutionary dynamics using TreeTime
• bio-epidemiological-genomics-transmission-inferenceInfer pathogen transmission networks and identify likely transmission pairs usin
• bio-epidemiological-genomics-variant-surveillanceAssign pathogen lineages and track variants using Nextclade and pangolin for vir
• bio-epitranscriptomics-m6a-differential
• bio-epitranscriptomics-m6a-peak-calling
• bio-epitranscriptomics-m6anet-analysis
• bio-epitranscriptomics-merip-preprocessing
• bio-epitranscriptomics-modification-visualization
• bio-experimental-design-batch-design
• bio-experimental-design-multiple-testing
• bio-experimental-design-power-analysis
• bio-experimental-design-sample-size
• bio-expression-matrix-counts-ingest
• bio-expression-matrix-gene-id-mapping
• bio-expression-matrix-metadata-joins
• bio-expression-matrix-sparse-handling
• bio-fastq-qualityWork with FASTQ quality scores using Biopython. Use when analyzing read quality,
• bio-filter-sequencesFilter and select sequences by criteria (length, ID, GC content, patterns) using
• bio-flow-cytometry-bead-normalizationBead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ
• bio-flow-cytometry-clustering-phenotypingUnsupervised clustering and cell type identification for flow/mass cytometry. Co
• bio-flow-cytometry-compensation-transformationSpillover compensation and data transformation for flow cytometry. Covers compen
• bio-flow-cytometry-cytometry-qcComprehensive quality control for flow cytometry and CyTOF data. Covers flow rat
• bio-flow-cytometry-differential-analysisDifferential abundance and state analysis for cytometry data. Compare cell popul
• bio-flow-cytometry-doublet-detectionDetect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gat
• bio-flow-cytometry-fcs-handlingRead and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, ac
• bio-flow-cytometry-gating-analysisManual and automated gating for defining cell populations in flow cytometry. Cov
• bio-format-conversionConvert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopyt
• bio-fragment-analysisAnalyzes cfDNA fragment size distributions and fragmentomics features using Fina
• bio-gatk-variant-callingVariant calling with GATK HaplotypeCaller following best practices. Covers germl
• bio-genome-assembly-assembly-polishing
• bio-genome-assembly-assembly-qc
• bio-genome-assembly-contamination-detection
• bio-genome-assembly-hifi-assembly
• bio-genome-assembly-long-read-assembly
• bio-genome-assembly-metagenome-assembly
• bio-genome-assembly-scaffolding
• bio-genome-assembly-short-read-assembly
• bio-genome-engineering-base-editing-designDesign guides for cytosine and adenine base editing using editing window optimiz
• bio-genome-engineering-grna-designDesign guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local
• bio-genome-engineering-hdr-template-designDesign homology-directed repair donor templates for CRISPR knock-ins using prime
• bio-genome-engineering-off-target-predictionPredict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. I
• bio-genome-engineering-prime-editing-designDesign pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer,
• bio-genome-intervals-bed-file-basics
• bio-genome-intervals-bigwig-tracks
• bio-genome-intervals-coverage-analysis
• bio-genome-intervals-gtf-gff-handling
• bio-genome-intervals-interval-arithmetic
• bio-genome-intervals-proximity-operations
• bio-geo-data
• bio-hi-c-analysis-compartment-analysisDetect A/B compartments from Hi-C data using cooltools and eigenvector decomposi
• bio-hi-c-analysis-contact-pairsProcess Hi-C read pairs using pairtools. Parse alignments, filter duplicates, cl
• bio-hi-c-analysis-hic-data-ioLoad, convert, and manipulate Hi-C contact matrices using cooler format. Read .c
• bio-hi-c-analysis-hic-differentialCompare Hi-C contact matrices between conditions to identify differential chroma
• bio-hi-c-analysis-hic-visualizationVisualize Hi-C contact matrices, TADs, loops, and genomic features using matplot
• bio-hi-c-analysis-loop-callingDetect chromatin loops and point interactions from Hi-C data using cooltools, ch
• bio-hi-c-analysis-matrix-operationsBalance, normalize, and transform Hi-C contact matrices using cooler and cooltoo
• bio-hi-c-analysis-tad-detectionCall topologically associating domains (TADs) from Hi-C data using insulation sc
• bio-imaging-mass-cytometry-cell-segmentationCell segmentation from multiplexed tissue images. Covers deep learning (Cellpose
• bio-imaging-mass-cytometry-data-preprocessingLoad and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF
• bio-imaging-mass-cytometry-interactive-annotationInteractive cell type annotation for IMC data. Covers napari-based annotation, m
• bio-imaging-mass-cytometry-phenotypingCell type assignment from marker expression in IMC data. Covers manual gating, c
• bio-imaging-mass-cytometry-quality-metricsQuality metrics for IMC data including signal-to-noise, channel correlation, tis
• bio-imaging-mass-cytometry-spatial-analysisSpatial analysis of cell neighborhoods and interactions in IMC data. Covers neig
• bio-immunoinformatics-epitope-predictionPredict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-bas
• bio-immunoinformatics-immunogenicity-scoringScore and prioritize neoantigens and epitopes for immunogenicity using multi-fac
• bio-immunoinformatics-mhc-binding-predictionPredict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpa
• bio-immunoinformatics-neoantigen-predictionIdentify tumor neoantigens from somatic mutations using pVACtools for personaliz
• bio-immunoinformatics-tcr-epitope-bindingPredict TCR-epitope specificity using ERGO-II and deep learning models for T-cel
• bio-isoform-switchingAnalyzes isoform switching events and functional consequences using IsoformSwitc
• bio-liquid-biopsy-pipeline
• bio-local-blast
• bio-long-read-sequencing-clair3-variantsDeep learning-based variant calling from long reads using Clair3 for SNPs and sm
• bio-long-read-sequencing-isoseq-analysisAnalyze PacBio Iso-Seq data for full-length isoform discovery and quantification
• bio-long-read-sequencing-nanopore-methylationCalls DNA methylation from Oxford Nanopore sequencing data using signal-level an
• bio-longitudinal-monitoringTracks ctDNA dynamics over time for treatment response monitoring using serial l
• bio-longread-alignmentAlign long reads using minimap2 for Oxford Nanopore and PacBio data. Supports va
• bio-longread-medakaPolish assemblies and call variants from Oxford Nanopore data using medaka. Uses
• bio-longread-qcQuality control for long-read sequencing data using NanoPlot, NanoStat, and chop
• bio-longread-structural-variantsDetect structural variants from long-read alignments using Sniffles, cuteSV, and
• bio-machine-learning-atlas-mapping
• bio-machine-learning-biomarker-discovery
• bio-machine-learning-model-validation
• bio-machine-learning-omics-classifiers
• bio-machine-learning-prediction-explanation
• bio-machine-learning-survival-analysis
• bio-metabolomics-lipidomicsSpecialized lipidomics analysis for lipid identification, quantification, and pa
• bio-metabolomics-metabolite-annotationMetabolite identification from m/z and retention time. Covers database matching,
• bio-metabolomics-msdial-preprocessingMS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak det
• bio-metabolomics-normalization-qcQuality control and normalization for metabolomics data. Covers QC-based correct
• bio-metabolomics-pathway-mappingMap metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst.
• bio-metabolomics-statistical-analysisStatistical analysis for metabolomics data. Covers univariate testing, multivari
• bio-metabolomics-targeted-analysisTargeted metabolomics analysis using MRM/SRM with standard curves. Covers absolu
• bio-metabolomics-xcms-preprocessingXCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, r
• bio-metagenomics-abundanceSpecies abundance estimation using Bracken with Kraken2 output. Redistributes re
• bio-metagenomics-amr-detectionDetect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD.
• bio-metagenomics-functional-profilingProfile functional potential of metagenomes using HUMAnN3 and similar tools. Use
• bio-metagenomics-krakenTaxonomic classification of metagenomic reads using Kraken2. Fast k-mer based cl
• bio-metagenomics-metaphlanMarker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate speci
• bio-metagenomics-strain-trackingTrack bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare gen
• bio-metagenomics-visualizationVisualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplo
• bio-methylation-based-detectionAnalyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bi
• bio-methylation-bismark-alignmentBisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles g
• bio-methylation-callingExtract methylation calls from Bismark BAM files using bismark_methylation_extra
• bio-methylation-dmr-detectionDifferentially methylated region (DMR) detection using methylKit tiles, bsseq BS
• bio-methylation-methylkitDNA methylation analysis with methylKit in R. Import Bismark coverage files, fil
• bio-microbiome-amplicon-processingAmplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequenci
• bio-microbiome-differential-abundanceDifferential abundance testing for microbiome data using compositionally-aware m
• bio-microbiome-diversity-analysisAlpha and beta diversity analysis for microbiome data. Calculate within-sample r
• bio-microbiome-functional-predictionPredict metagenome functional content from 16S rRNA marker gene data using PICRU
• bio-microbiome-qiime2-workflowQIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2
• bio-microbiome-taxonomy-assignmentTaxonomic classification of ASVs using reference databases like SILVA, GTDB, or
• bio-molecular-descriptorsCalculates molecular descriptors and fingerprints using RDKit. Computes Morgan f
• bio-molecular-ioReads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) usin
• bio-motif-search
• bio-multi-omics-data-harmonizationPreprocessing and harmonization of multi-omics data before integration. Covers n
• bio-multi-omics-mixomics-analysisSupervised and unsupervised multi-omics integration with mixOmics. Includes sPLS
• bio-multi-omics-mofa-integrationMulti-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple dat
• bio-multi-omics-similarity-networkSimilarity Network Fusion (SNF) for patient stratification using multi-omics dat
• bio-orchestratorMeta-agent that routes bioinformatics requests to specialised sub-skills. Handle
• bio-paired-end-fastqHandle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Ill
• bio-pathway-enrichment-visualizationVisualize enrichment results using enrichplot package functions. Use when creati
• bio-pathway-go-enrichmentGene Ontology over-representation analysis using clusterProfiler enrichGO. Use w
• bio-pathway-gseaGene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when a
• bio-pathway-kegg-pathwaysKEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and
• bio-pathway-reactomeReactome pathway enrichment using ReactomePA package. Use when analyzing gene li
• bio-pathway-wikipathwaysWikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyz
• bio-pdb-geometric-analysisPerform geometric calculations on protein structures using Biopython Bio.PDB. Us
• bio-pdb-structure-ioParse and write protein structure files using Biopython Bio.PDB. Use when readin
• bio-pdb-structure-modificationModify protein structures using Biopython Bio.PDB. Use when transforming coordin
• bio-pdb-structure-navigationNavigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use wh
• bio-phasing-imputation-genotype-imputation
• bio-phasing-imputation-haplotype-phasing
• bio-phasing-imputation-imputation-qc
• bio-phasing-imputation-reference-panels
• bio-phylo-distance-calculations
• bio-phylo-modern-tree-inference
• bio-phylo-tree-io
• bio-phylo-tree-manipulation
• bio-phylo-tree-visualization
• bio-pileup-generation
• bio-population-genetics-association-testing
• bio-population-genetics-linkage-disequilibrium
• bio-population-genetics-plink-basics
• bio-population-genetics-population-structure
• bio-population-genetics-scikit-allel-analysis
• bio-population-genetics-selection-statistics
• bio-primer-design-primer-basics
• bio-primer-design-primer-validation
• bio-primer-design-qpcr-primers
• bio-proteomics-data-importLoad and parse mass spectrometry data formats including mzML, mzXML, and quantif
• bio-proteomics-dia-analysisData-independent acquisition (DIA) proteomics analysis with DIA-NN and other too
• bio-proteomics-differential-abundanceStatistical testing for differentially abundant proteins between conditions. Cov
• bio-proteomics-peptide-identificationPeptide-spectrum matching and protein identification from MS/MS data. Use when i
• bio-proteomics-protein-inferenceProtein grouping and inference from peptide identifications. Use when resolving
• bio-proteomics-proteomics-qcQuality control and assessment for proteomics data. Use when evaluating proteomi
• bio-proteomics-ptm-analysisPost-translational modification analysis including phosphorylation, acetylation,
• bio-proteomics-quantificationProtein quantification from mass spectrometry data including label-free (LFQ, in
• bio-proteomics-spectral-librariesBuild, manage, and search spectral libraries for proteomics. Use when creating o
• bio-reaction-enumerationEnumerates chemical libraries through reaction SMARTS transformations using RDKi
• bio-read-alignment-bowtie2-alignment
• bio-read-alignment-bwa-alignment
• bio-read-alignment-hisat2-alignment
• bio-read-alignment-star-alignment
• bio-read-qc-adapter-trimmingRemove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supp
• bio-read-qc-contamination-screeningDetect sample contamination and cross-species reads using FastQ Screen. Screen r
• bio-read-qc-fastp-workflowAll-in-one read preprocessing with fastp including adapter trimming, quality fil
• bio-read-qc-quality-filteringFilter reads by quality scores, length, and N content using Trimmomatic and fast
• bio-read-qc-quality-reportsGenerate and interpret quality reports from FASTQ files using FastQC and MultiQC
• bio-read-qc-umi-processingExtract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs
• bio-read-sequencesRead biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Bio
• bio-reference-operations
• bio-reporting-automated-qc-reports
• bio-reporting-figure-export
• bio-reporting-jupyter-reports
• bio-reporting-quarto-reports
• bio-reporting-rmarkdown-reports
• bio-research-tools-biomarker-signature-studio
• bio-restriction-enzyme-selection
• bio-restriction-fragment-analysis
• bio-restriction-mapping
• bio-restriction-sites
• bio-reverse-complement
• bio-ribo-seq-orf-detectionDetect and quantify translated ORFs from Ribo-seq data including uORFs and novel
• bio-ribo-seq-riboseq-preprocessingPreprocess ribosome profiling data including adapter trimming, size selection, r
• bio-ribo-seq-ribosome-periodicityValidate Ribo-seq data quality by checking 3-nucleotide periodicity and calculat
• bio-ribo-seq-ribosome-stallingDetect ribosome pausing and stalling sites from Ribo-seq data at codon resolutio
• bio-ribo-seq-translation-efficiencyCalculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA
• bio-rna-quantification-alignment-free-quant
• bio-rna-quantification-count-matrix-qc
• bio-rna-quantification-featurecounts-counting
• bio-rna-quantification-tximport-workflow
• bio-rnaseq-qcRNA-seq specific quality control including rRNA contamination detection, strande
• bio-sam-bam-basics
• bio-sashimi-plotsCreates sashimi plots showing RNA-seq read coverage and splice junction counts u
• bio-seq-objects
• bio-sequence-properties
• bio-sequence-similarity
• bio-sequence-slicing
• bio-sequence-statisticsCalculate sequence statistics (N50, length distribution, GC content, summary rep
• bio-similarity-searchingPerforms molecular similarity searches using Tanimoto coefficient on fingerprint
• bio-single-cell-batch-integrationIntegrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors
• bio-single-cell-cell-annotationAutomated cell type annotation using reference-based methods including CellTypis
• bio-single-cell-cell-communicationInfer cell-cell communication networks from scRNA-seq data using CellChat, Niche
• bio-single-cell-clusteringDimensionality reduction and clustering for single-cell RNA-seq using Seurat (R)
• bio-single-cell-data-ioRead, write, and create single-cell data objects using Seurat (R) and Scanpy (Py
• bio-single-cell-doublet-detectionDetect and remove doublets (multiple cells captured in one droplet) from single-
• bio-single-cell-lineage-tracingReconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial muta
• bio-single-cell-markers-annotationFind marker genes and annotate cell types in single-cell RNA-seq using Seurat (R
• bio-single-cell-metabolite-communicationAnalyze metabolite-mediated cell-cell communication using MeboCost for metabolic
• bio-single-cell-multimodal-integrationAnalyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when wor
• bio-single-cell-perturb-seqAnalyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq
• bio-single-cell-preprocessingQuality control, filtering, and normalization for single-cell RNA-seq using Seur
• bio-single-cell-scatac-analysisSingle-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Geno
• bio-single-cell-splicingAnalyzes alternative splicing at single-cell resolution using BRIE2 for probabil
• bio-single-cell-trajectory-inferenceInfer developmental trajectories and pseudotime from single-cell RNA-seq data us
• bio-small-rna-seq-differential-mirna
• bio-small-rna-seq-mirdeep2-analysis
• bio-small-rna-seq-mirge3-analysis
• bio-small-rna-seq-smrna-preprocessing
• bio-small-rna-seq-target-prediction
• bio-spatial-transcriptomics-image-analysisProcess and analyze tissue images from spatial transcriptomics data using Squidp
• bio-spatial-transcriptomics-spatial-communicationAnalyze cell-cell communication in spatial transcriptomics data using ligand-rec
• bio-spatial-transcriptomics-spatial-data-ioLoad spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and o
• bio-spatial-transcriptomics-spatial-deconvolutionEstimate cell type composition in spatial transcriptomics spots using reference-
• bio-spatial-transcriptomics-spatial-domainsIdentify spatial domains and tissue regions in spatial transcriptomics data usin
• bio-spatial-transcriptomics-spatial-multiomicsAnalyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium
• bio-spatial-transcriptomics-spatial-neighborsBuild spatial neighbor graphs for spatial transcriptomics data using Squidpy. Co
• bio-spatial-transcriptomics-spatial-preprocessingQuality control, filtering, normalization, and feature selection for spatial tra
• bio-spatial-transcriptomics-spatial-proteomicsAnalyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including c
• bio-spatial-transcriptomics-spatial-statisticsCompute spatial statistics for spatial transcriptomics data using Squidpy. Calcu
• bio-spatial-transcriptomics-spatial-visualizationVisualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue p
• bio-splicing-pipeline
• bio-splicing-qcAssesses RNA-seq data quality for splicing analysis including junction saturatio
• bio-splicing-quantificationQuantifies alternative splicing events (PSI/percent spliced in) from RNA-seq usi
• bio-sra-data
• bio-structural-biology-alphafold-predictionsAccess and analyze AlphaFold protein structure predictions. Use when predicted s
• bio-structural-biology-modern-structure-predictionPredict protein structures using modern ML models including AlphaFold3, ESMFold,
• bio-substructure-searchSearches molecular libraries for substructure matches using SMARTS patterns with
• bio-systems-biology-context-specific-models
• bio-systems-biology-flux-balance-analysis
• bio-systems-biology-gene-essentiality
• bio-systems-biology-metabolic-reconstruction
• bio-systems-biology-model-curation
• bio-tcr-bcr-analysis-immcantation-analysisAnalyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell p
• bio-tcr-bcr-analysis-mixcr-analysisPerform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data usin
• bio-tcr-bcr-analysis-repertoire-visualizationCreate publication-quality visualizations of immune repertoire data including ci
• bio-tcr-bcr-analysis-scirpy-analysisAnalyze single-cell TCR and BCR data integrated with gene expression using scirp
• bio-tcr-bcr-analysis-vdjtools-analysisCalculate immune repertoire diversity metrics, compare samples, and track clonal
• bio-transcription-translation
• bio-tumor-fraction-estimationEstimates circulating tumor DNA fraction from shallow whole-genome sequencing us
• bio-uniprot-access
• bio-variant-annotationComprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and A
• bio-variant-callingCall SNPs and indels from aligned reads using bcftools mpileup and call. Use whe
• bio-variant-calling-clinical-interpretationClinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicit
• bio-variant-calling-deepvariantDeep learning-based variant calling with Google DeepVariant. Provides high accur
• bio-variant-calling-filtering-best-practicesComprehensive variant filtering including GATK VQSR, hard filters, bcftools expr
• bio-variant-calling-joint-callingJoint genotype calling across multiple samples using GATK CombineGVCFs and Genot
• bio-variant-calling-structural-variant-callingCall structural variants (SVs) from short-read sequencing using Manta, Delly, an
• bio-variant-normalizationNormalize indel representation and split multiallelic variants using bcftools no
• bio-vcf-basicsView, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use
• bio-vcf-manipulationMerge, concatenate, sort, intersect, and subset VCF files using bcftools. Use wh
• bio-vcf-statisticsGenerate variant statistics, sample concordance, and quality metrics using bcfto
• bio-virtual-screeningPerforms structure-based virtual screening using AutoDock Vina 1.2 for molecular
• bio-workflow-management-cwl-workflows
• bio-workflow-management-nextflow-pipelines
• bio-workflow-management-snakemake-workflows
• bio-workflow-management-wdl-workflows
• bio-workflows-atacseq-pipeline
• bio-workflows-biomarker-pipeline
• bio-workflows-chipseq-pipeline
• bio-workflows-clip-pipeline
• bio-workflows-cnv-pipeline
• bio-workflows-crispr-editing-pipeline
• bio-workflows-crispr-screen-pipeline
• bio-workflows-cytometry-pipeline
• bio-workflows-expression-to-pathways
• bio-workflows-fastq-to-variants
• bio-workflows-genome-assembly-pipeline
• bio-workflows-gwas-pipeline
• bio-workflows-hic-pipeline
• bio-workflows-imc-pipeline
• bio-workflows-longread-sv-pipeline
• bio-workflows-merip-pipeline
• bio-workflows-metabolic-modeling-pipeline
• bio-workflows-metabolomics-pipeline
• bio-workflows-metagenomics-pipeline
• bio-workflows-methylation-pipeline
• bio-workflows-microbiome-pipeline
• bio-workflows-multi-omics-pipeline
• bio-workflows-multiome-pipeline
• bio-workflows-neoantigen-pipeline
• bio-workflows-outbreak-pipeline
• bio-workflows-proteomics-pipeline
• bio-workflows-riboseq-pipeline
• bio-workflows-rnaseq-to-de
• bio-workflows-scrnaseq-pipeline
• bio-workflows-smrna-pipeline
• bio-workflows-somatic-variant-pipeline
• bio-workflows-spatial-pipeline
• bio-workflows-tcr-pipeline
• bio-write-sequencesWrite biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopytho
• bioinformatics-singlecell
• biokernel
• biologist-analyst|
• biomaster-workflows
• biomcp-server
• biomedical-data-analysis
• biomedical-searchComplete biomedical information search combining PubMed, preprints, clinical tri
• biomniAutonomous biomedical AI agent framework for executing complex research tasks ac
• biomni-general-agent
• biomni-research-agent
• biopythonPrimary Python toolkit for molecular biology. Preferred for Python-based PubMed/
• biorxiv-databaseEfficient database search tool for bioRxiv preprint server. Use this skill when
• bioservicesPrimary Python tool for 40+ bioinformatics services. Preferred for multi-databas
• boltz>
• boltzgen>
• bone-marrow-ai-agent
• brainstormingYou MUST use this before any creative work - creating features, building compone
• brenda-databaseAccess BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kca
• bulk-rna-seq-batch-correction-with-combatUse omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-se
• bulk-rna-seq-differential-expression-with-omicverseGuide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping
• bulk-rna-seq-deseq2-analysis-with-omicverseWalk Claude through PyDESeq2-based differential expression, including ID mapping
• string-protein-interaction-analysis-with-omicverseHelp Claude query STRING for protein interactions, build PPI graphs with pyPPI,
• bulk-rna-seq-deconvolution-with-bulk2singleTurn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's
• bulktrajblend-trajectory-interpolationExtend scRNA-seq developmental trajectories with BulkTrajBlend by generating int
• bulk-wgcna-analysis-with-omicverseAssist Claude in running PyWGCNA through omicverse—preprocessing expression matr
• cancer-metabolism-agent
• care-coordination
• cart-design-optimizer-agent
• cbioportal-databaseQuery cBioPortal for cancer genomics data including somatic mutations, copy numb
• cell-free-expression>
• cellagent-annotation
• cellfree-rna-agent
• cellular-senescence-agent
• cellxgene-censusQuery CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retr
• chai>
• chatehr-clinician-assistant
• chematagent-drug-discovery
• chembl-databaseQuery ChEMBL's bioactive molecules and drug discovery data. Search compounds by
• chembl-searchSearch ChEMBL bioactive molecules database with natural language queries. Find c
• chemcrow-drug-discovery
• chemical-property-lookup
• chemist-analyst|
• chemistry-agent
• chip-clonal-hematopoiesis-agent
• chromosomal-instability-agent
• citation-managementComprehensive citation management for academic research. Search Google Scholar a
• claims-appeals
• claw-ancestry-pcaAncestry decomposition PCA against the Simons Genome Diversity Project
• claw-metagenomicsShotgun metagenomics profiling — taxonomy, resistome, and functional pathways
• claw-semantic-simSemantic Similarity Index for disease research literature using PubMedBERT embed
• clinical-decision-supportGenerate professional clinical decision support (CDS) documents for pharmaceutic
• clinical-diagnostic-reasoningIdentify and counteract cognitive biases in medical decision-making through syst
• clinical-nlp-extractor
• clinical-note-summarization
• clinical-reportsWrite comprehensive clinical reports including case reports (CARE guidelines), d
• clinical-trial-protocol-skillGenerate clinical trial protocols for medical devices or drugs. This skill shoul
• clinical-trials-searchSearch ClinicalTrials.gov with natural language queries. Find clinical trials, e
• clinicaltrials-databaseQuery ClinicalTrials.gov via API v2. Search trials by condition, drug, location,
• clinpgxQuery the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations,
• clinpgx-databaseAccess ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug in
• clinvar-databaseQuery NCBI ClinVar for variant clinical significance. Search by gene/position, i
• cnv-caller-agent
• coagulation-thrombosis-agent
• cobrapyConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux samp
• compbioagent-explorer
• computational-pathology-agent
• convergence-studySpatial and temporal convergence analysis with Richardson extrapolation and Grid
• cosmic-databaseAccess COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Cen
• crisis-detection-intervention-aiDetect crisis signals in user content using NLP, mental health sentiment analysi
• crisis-response-protocolHandle mental health crisis situations in AI coaching safely. Use when implement
• crispr-guide-design
• crispr-offtarget-predictor
• cryoem-ai-drug-design-agent
• ctdna-dynamics-mrd-agent
• cytokine-storm-analysis-agent
• daskDistributed computing for larger-than-RAM pandas/NumPy workflows. Use when you n
• data-stats-analysisPerform statistical tests, hypothesis testing, correlation analysis, and multipl
• data-transformTransform, clean, reshape, and preprocess data using pandas and numpy. Works wit
• data-visualization-biomedical
• data-visualization-expert
• data-viz-plotsCreate publication-quality plots and visualizations using matplotlib and seaborn
• datacommons-clientWork with Data Commons, a platform providing programmatic access to public stati
• datamolPythonic wrapper around RDKit with simplified interface and sensible defaults. P
• deep-researchExecute autonomous multi-step deep research on any topic. Use when the user asks
• deep-research-swarm
• deep-visual-proteomics-agent
• deepchemMolecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs
• deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprin
• depmapQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency sc
• diffdockDiffusion-based molecular docking. Predict protein-ligand binding poses from PDB
• differentiation-schemesSelect and apply numerical differentiation schemes for PDE/ODE discretization. U
• digital-twin-clinical-agent
• dispatching-parallel-agentsUse when facing 2+ independent tasks that can be worked on without shared state
• dnanexus-integrationDNAnexus cloud genomics platform. Build apps/applets, manage data (upload/downlo
• doc-coauthoringGuide users through a structured workflow for co-authoring documentation. Use wh
• docxUse this skill whenever the user wants to create, read, edit, or manipulate Word
• docxComprehensive document creation, editing, and analysis with support for tracked
• drug-discovery-searchEnd-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets
• drug-interaction-checker
• drug-labels-searchSearch FDA drug labels with natural language queries. Official drug information,
• drug-photoMedication photo to personalised PGx dosage card via Claude vision — snap a pill
• drugbank-databaseAccess and analyze comprehensive drug information from the DrugBank database inc
• drugbank-searchSearch DrugBank comprehensive drug database with natural language queries. Drug
• ehr-fhir-integration
• emergency-card生成紧急情况下快速访问的医疗信息摘要卡片。当用户需要旅行、就诊准备、紧急情况或询问"紧急信息"、"医疗卡片"、"急救信息"时使用此技能。提取关键信息（过敏、用药
• ena-databaseAccess European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw
• ensembl-databaseQuery Ensembl genome database REST API for 250+ species. Gene lookups, sequence
• epidemiologist-analyst|
• epigenomics-methylgpt-agent
• equity-scorerCompute HEIM diversity and equity metrics from VCF or ancestry data. Generates h
• esmComprehensive toolkit for protein language models including ESM3 (generative mul
• etetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary ev
• executing-plansUse when you have a written implementation plan to execute in a separate session
• exosome-ev-analysis-agent
• exploratory-data-analysisPerform comprehensive exploratory data analysis on scientific data files across
• family-health-analyzer分析家族病史、评估遗传风险、识别家庭健康模式、提供个性化预防建议
• fastq-analysis-pipelineGuide through omicverse's alignment module for SRA downloading, FASTQ quality co
• fda-databaseQuery openFDA API for drugs, devices, adverse events, recalls, regulatory submis
• fhir-developer-skill>
• fhir-development
• find-skillsHelps users discover and install agent skills when they ask questions like "how
• finishing-a-development-branchUse when implementation is complete, all tests pass, and you need to decide how
• fitness-analyzer分析运动数据、识别运动模式、评估健身进展，并提供个性化训练建议。支持与慢性病数据的关联分析。
• flowioParse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arra
• foldseek>
• galaxy-bridgeGalaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinf
• gene-databaseQuery NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene
• gene-panel-design-agent
• genimlThis skill should be used when working with genomic interval data (BED files) fo
• genome-compareCompare your genome to George Church (PGP-1) and estimate ancestry composition v
• geo-databaseAccess NCBI GEO for gene expression/genomics data. Search/download microarray an
• geopandasPython library for working with geospatial vector data including shapefiles, Geo
• ggetCLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST s
• ginkgo-cloud-labSubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a w
• glycoengineeringAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation s
• gnomad-databaseQuery gnomAD (Genome Aggregation Database) for population allele frequencies, va
• goal-analyzer分析健康目标数据、识别目标模式、评估目标进度,并提供个性化目标管理建议。支持与营养、运动、睡眠等健康数据的关联分析。
• grief-companionCompassionate bereavement support, memorial creation, grief education, and heali
• gsea-enrichment-analysisGene set enrichment analysis with correct geneset format handling. Critical guid
• gtarsHigh-performance toolkit for genomic interval analysis in Rust with Python bindi
• gtex-databaseQuery GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expressi
• gwas-databaseQuery NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs I
• gwas-lookupFederated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets
• gwas-prsCalculate polygenic risk scores from DTC genetic data using the PGS Catalog
• health-trend-analyzer分析一段时间内健康数据的趋势和模式。关联药物、症状、生命体征、化验结果和其他健康指标的变化。识别令人担忧的趋势、改善情况，并提供数据驱动的洞察。当用户询问健康趋
• hemoglobinopathy-analysis-agent
• hipaa-complianceEnsure HIPAA compliance when handling PHI (Protected Health Information). Use wh
• histolabDigital pathology image processing toolkit for whole slide images (WSI). Use thi
• hmdb-databaseAccess Human Metabolome Database (220K+ metabolites). Search by name/ID/structur
• hrd-analysis-agent
• hrv-alexithymia-expertHeart rate variability biometrics and emotional awareness training. Expert in HR
• hypogenicAutomated hypothesis generation and testing using large language models. Use thi
• hypothesis-generationGenerate testable hypotheses. Formulate from observations, design experiments, e
• imaging-data-commonsQuery and download public cancer imaging data from NCI Imaging Data Commons usin
• immune-checkpoint-combination-agent
• infographicsCreate professional infographics using Nano Banana Pro AI with smart iterative r
• instrument-data-to-allotropeConvert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope S
• interpro-databaseQuery InterPro for protein family, domain, and functional site annotations. Inte
• ipsae>
• iso-13485-certificationComprehensive toolkit for preparing ISO 13485 certification documentation for me
• jaspar-databaseQuery JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs).
• jungian-psychologistExpert in Jungian analytical psychology, depth psychology, shadow work, archetyp
• kegg-databaseDirect REST API access to KEGG (academic use only). Pathway analysis, gene-pathw
• knowledge-synthesis
• kragen-knowledge-graph
• lab-results
• labarchive-integrationElectronic lab notebook API integration. Access notebooks, manage entries/attach
• labstepInteract with the Labstep electronic lab notebook API using labstepPy. Query exp
• lamindbThis skill should be used when working with LaminDB, an open-source data framewo
• latchbio-integrationLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @wo
• latex-postersCreate professional research posters in LaTeX using beamerposter, tikzposter, or
• leads-literature-mining
• ligandmpnn>
• linear-solversSelect and configure linear solvers for systems Ax=b in dense and sparse problem
• liquid-biopsy-analytics-agent
• lit-synthesizerSearch PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and
• literature-reviewConduct comprehensive, systematic literature reviews using multiple academic dat
• literature-searchComprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxi
• lobster-bioinformaticsRun bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq
• long-read-sequencing-agent
• mage-antibody-generator
• markdown-mermaid-writingComprehensive markdown and Mermaid diagram writing skill. Use when creating any
• markitdownConvert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX,
• matchmsMass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, m
• matplotlibLow-level plotting library for full customization. Use when you need fine-graine
• mcpmed-bioinformatics-serverModel Context Protocol (MCP) server for bioinformatics web services like GEO, ST
• medchemMedicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS
• medea-therapeutic-discoveryAn AI agent for therapeutic discovery that executes transparent, multi-step omic
• medical-entity-extractorExtract medical entities (symptoms, medications, lab values, diagnoses) from pat
• medical-imaging-review>
• medical-research-toolkitQuery 14+ biomedical databases for drug repurposing, target discovery, clinical
• medical-specialty-briefsGenerate daily or on-demand medical research briefs for any medical specialty. S
• medrxiv-searchSearch medRxiv medical preprints with natural language queries. Powered by Valyu
• mental-health-analyzer分析心理健康数据、识别心理模式、评估心理健康状况、提供个性化心理健康建议。支持与睡眠、运动、营养等其他健康数据的关联分析。
• mesh-generationPlan and evaluate mesh generation for numerical simulations. Use when choosing g
• metabolomics-workbench-databaseAccess NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolit
• microbiome-cancer-agent
• modern-drug-rehab-computerComprehensive knowledge system for addiction recovery environments, supporting b
• molecular-dynamicsRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set u
• molecular-glue-discovery-agent
• molecule-evolution-agent
• molfeatMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pre
• monarch-databaseQuery the Monarch Initiative knowledge graph for disease-gene-phenotype associat
• mpn-progression-monitor-agent
• mpn-research-assistant
• mrd-edge-detection-agent
• multi-ancestry-prs-agent
• multi-search-engineMulti search engine integration with 17 engines (8 CN + 9 Global). Supports adva
• multimodal-medical-imaging
• multimodal-radpath-fusion-agent
• myeloma-mrd-agent
• networkxComprehensive toolkit for creating, analyzing, and visualizing complex networks
• neurokit2Comprehensive biosignal processing toolkit for analyzing physiological data incl
• neuropixels-analysisNeuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess,
• nextflow-developmentRun nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data
• ngs-analysis
• nicheformer-spatial-agent
• nk-cell-therapy-agent
• nonlinear-solversSelect and configure nonlinear solvers for f(x)=0 or min F(x). Use for Newton me
• numerical-integrationSelect and configure time integration methods for ODE/PDE simulations. Use when
• numerical-stabilityAnalyze and enforce numerical stability for time-dependent PDE simulations. Use
• nutrition-analyzer分析营养数据、识别营养模式、评估营养状况，并提供个性化营养建议。支持与运动、睡眠、慢性病数据的关联分析。
• occupational-health-analyzer分析职业健康数据、识别工作相关健康风险、评估职业健康状况、提供个性化职业健康建议。支持与睡眠、运动、心理健康等其他健康数据的关联分析。
• omero-integrationMicroscopy data management platform. Access images via Python, retrieve datasets
• ontology-explorer>
• ontology-mapper>
• ontology-validator>
• open-notebookSelf-hosted, open-source alternative to Google NotebookLM for AI-powered researc
• open-targets-searchSearch Open Targets drug-disease associations with natural language queries. Tar
• openalex-databaseQuery and analyze scholarly literature using the OpenAlex database. This skill s
• opentargets-databaseQuery Open Targets Platform for target-disease associations, drug target discove
• opentrons-integrationLab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, l
• opentrons-protocol-agent
• organoid-drug-response-agent
• pan-cancer-multiomics-agent
• paper-2-webThis skill should be used when converting academic papers into promotional and p
• parameter-optimizationExplore and optimize simulation parameters via design of experiments (DOE), sens
• patents-searchSearch global patents with natural language queries. Prior art, patent landscape
• pathmlComputational pathology toolkit for analyzing whole-slide images (WSI) and multi
• patiently-aiPatiently AI simplifies medical documents for patients. Takes doctor's letters,
• pdb>
• pdb-databaseAccess RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/
• pdfUse this skill whenever the user wants to do anything with PDF files. This inclu
• pdfComprehensive PDF manipulation toolkit for extracting text and tables, creating
• pdf-processingExtract text and tables from PDF files, fill forms, merge documents. Use when wo
• pdf-processing-proProduction-ready PDF processing with forms, tables, OCR, validation, and batch o
• pdx-model-analysis-agent
• peer-reviewSystematic peer review toolkit. Evaluate methodology, statistics, design, reprod
• performance-profilingIdentify computational bottlenecks, analyze scaling behavior, estimate memory re
• perplexity-searchPerform AI-powered web searches with real-time information using Perplexity mode
• pharmacogenomics-agent
• pharmgx-reporterPharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 3
• phylogeneticsBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2
• plotlyInteractive visualization library. Use when you need hover info, zoom, pan, or w
• polarsFast in-memory DataFrame library for datasets that fit in RAM. Use when pandas i
• popeve-variant-predictor-agent
• post-processingExtract, analyze, and visualize simulation output data. Use for field extraction
• pptxUse this skill any time a .pptx file is involved in any way — as input, output,
• pptxPresentation creation, editing, and analysis. When Claude needs to work with pre
• pptx-postersCreate research posters using HTML/CSS that can be exported to PDF or PPTX. Use
• precision-oncology-agent
• prior-auth-coworker
• prior-auth-review-skillAutomate payer review of prior authorization (PA) requests. This skill should be
• profile-report>-
• protac-design-agent
• protein-design-workflow>
• protein-qc>
• protein-structure-prediction
• proteinmpnn>
• protocolsio-integrationIntegration with protocols.io API for managing scientific protocols. This skill
• prs-net-deep-learning-agent
• psychologist-analyst|
• pubchem-databaseQuery PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/S
• pubmed-databaseDirect REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API
• pubmed-searchSearch PubMed for scientific literature. Use when the user asks to find papers,
• pydeseq2Differential gene expression analysis (Python DESeq2). Identify DE genes from bu
• pydicomPython library for working with DICOM (Digital Imaging and Communications in Med
• pyhealthComprehensive healthcare AI toolkit for developing, testing, and deploying machi
• pylabrobotLaboratory automation toolkit for controlling liquid handlers, plate readers, pu
• pymc-bayesian-modelingBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational
• pymooMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts
• pyopenmsPython interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS
• pysamGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FAST
• pytdcTherapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI
• pytorch-lightningDeep learning framework (PyTorch Lightning). Organize PyTorch code into Lightnin
• pyzoteroInteract with Zotero reference management libraries using the pyzotero Python cl
• radgpt-radiology-reporter
• radiomics-pathomics-fusion-agent
• rdkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing,
• reactome-databaseQuery Reactome REST API for pathway analysis, enrichment, gene-pathway mapping,
• receiving-code-reviewUse when receiving code review feedback, before implementing suggestions, especi
• recovery-community-moderatorTrauma-informed AI moderator for addiction recovery communities. Applies harm re
• regulatory-drafter
• regulatory-drafting
• rehabilitation-analyzer分析康复训练数据、识别康复模式、评估康复进展，并提供个性化康复建议
• repro-enforcerExport any bioinformatics analysis as a reproducible bundle with Conda environme
• requesting-code-reviewUse when completing tasks, implementing major features, or before merging to ver
• research-grantsWrite competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specif
• research-literature
• research-lookupLook up current research information using Perplexity's Sonar Pro Search or Sona
• rfdiffusion>
• rna-velocity-agent
• scanpySingle-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t
• scfoundation-model-agent
• scientific-brainstormingResearch ideation partner. Generate hypotheses, explore interdisciplinary connec
• scientific-critical-thinkingEvaluate research rigor. Assess methodology, experimental design, statistical va
• scientific-manuscript
• scientific-problem-selectionThis skill should be used when scientists need help with research problem select
• scientific-schematicsCreate publication-quality scientific diagrams using Nano Banana 2 AI with smart
• scientific-slidesBuild slide decks and presentations for research talks. Use this for making Powe
• scientific-visualizationCreate publication figures with matplotlib/seaborn/plotly. Multi-panel layouts,
• scientific-writingCore skill for the deep research and writing tool. Write scientific manuscripts
• scikit-bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, dive
• scikit-learnMachine learning in Python with scikit-learn. Use when working with supervised l
• scikit-survivalComprehensive toolkit for survival analysis and time-to-event modeling in Python
• scrna-orchestratorLocal Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery,
• scrna-qc
• scveloRNA velocity analysis with scVelo. Estimate cell state transitions from unsplice
• scvi-toolsThis skill should be used when working with single-cell omics data analysis usin
• seabornStatistical visualization with pandas integration. Use for quick exploration of
• search-strategy
• seq-wranglerSequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools
• shapModel interpretability and explainability using SHAP (SHapley Additive exPlanati
• simo-multiomics-integration-agent
• simpyProcess-based discrete-event simulation framework in Python. Use this skill when
• simulation-orchestratorOrchestrate multi-simulation campaigns including parameter sweeps, batch jobs, a
• simulation-validatorValidate simulations before, during, and after execution. Use for pre-flight che
• single-cell-annotation-skills-with-omicverseGuide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted
• single-cell-rna-qcPerforms quality control on single-cell RNA-seq data (.h5ad or .h5 files) using
• single-cell-cellphonedb-communication-mappingRun omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer li
• single-cell-clustering-and-batch-correction-with-omicverseGuide Claude through omicverse's single-cell clustering workflow, covering prepr
• single-cell-downstream-analysisChecklist-style reference for OmicVerse downstream tutorials covering AUCell sco
• single-cell-multi-omics-integrationQuick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA
• single-cell-preprocessing-with-omicverseWalk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data,
• single2spatial-spatial-mappingMap scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Sing
• single-trajectory-analysisGuide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA
• sleep-analyzer分析睡眠数据、识别睡眠模式、评估睡眠质量，并提供个性化睡眠改善建议。支持与其他健康数据的关联分析。
• slurm-job-script-generatorGenerate SLURM `sbatch` job scripts and sanity-check HPC resource requests (node
• solublempnn>
• spatial-agent
• spatial-epigenomics-agent
• spatial-transcriptomics-agent
• image-analysis
• spatial-communication
• spatial-data-io
• spatial-deconvolution
• spatial-domains
• spatial-multiomics
• spatial-neighbors
• spatial-preprocessing
• spatial-proteomics
• spatial-statistics
• spatial-visualization
• spatial-transcriptomics-analysis
• SpatialAgent
• STAgent
• spatial-transcriptomics-tutorials-with-omicverseGuide users through omicverse's spatial transcriptomics tutorials covering prepr
• speech-pathology-aiExpert speech-language pathologist specializing in AI-powered speech therapy, ph
• statistical-analysisStatistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regr
• statsmodelsStatistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis
• string-databaseQuery STRING API for protein-protein interactions (59M proteins, 20B interaction
• struct-predictorLocal protein structure prediction with AlphaFold, Boltz, or Chai. Compare predi
• subagent-driven-developmentUse when executing implementation plans with independent tasks in the current se
• systematic-debuggingUse when encountering any bug, test failure, or unexpected behavior, before prop
• tcell-exhaustion-analysis-agent
• tcga-bulk-data-preprocessing-with-omicverseGuide Claude through ingesting TCGA sample sheets, expression archives, and clin
• tcm-constitution-analyzer分析中医体质数据、识别体质类型、评估体质特征,并提供个性化养生建议。支持与营养、运动、睡眠等健康数据的关联分析。
• tcr-pmhc-prediction-agent
• tcr-repertoire-analysis-agent
• test-driven-developmentUse when implementing any feature or bugfix, before writing implementation code
• tiledbvcfEfficient storage and retrieval of genomic variant data using TileDB. Scalable V
• time-resolved-cryoem-agent
• time-steppingPlan and control time-step policies for simulations. Use when coupling CFL/physi
• timesfm-forecastingZero-shot time series forecasting with Google's TimesFM foundation model. Use fo
• tme-immune-profiling-agent
• tooluniverse-adverse-event-detectionDetect and analyze adverse drug event signals using FDA FAERS data, drug labels,
• tooluniverse-antibody-engineeringComprehensive antibody engineering and optimization for therapeutic development.
• tooluniverse-binder-discoveryDiscover novel small molecule binders for protein targets using structure-based
• tooluniverse-cancer-variant-interpretationProvide comprehensive clinical interpretation of somatic mutations in cancer. Gi
• tooluniverse-chemical-compound-retrievalRetrieves chemical compound information from PubChem and ChEMBL with disambiguat
• tooluniverse-chemical-safetyComprehensive chemical safety and toxicology assessment integrating ADMET-AI pre
• tooluniverse-clinical-guidelinesSearch and retrieve clinical practice guidelines across 12+ authoritative source
• tooluniverse-clinical-trial-designStrategic clinical trial design feasibility assessment using ToolUniverse. Evalu
• tooluniverse-clinical-trial-matchingAI-driven patient-to-trial matching for precision medicine and oncology. Given a
• tooluniverse-crispr-screen-analysisComprehensive CRISPR screen analysis for functional genomics. Analyze pooled or
• tooluniverse-disease-researchGenerate comprehensive disease research reports using 100+ ToolUniverse tools. C
• tooluniverse-drug-drug-interactionComprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyz
• tooluniverse-drug-repurposingIdentify drug repurposing candidates using ToolUniverse for target-based, compou
• tooluniverse-drug-researchGenerates comprehensive drug research reports with compound disambiguation, evid
• tooluniverse-drug-target-validationComprehensive computational validation of drug targets for early-stage drug disc
• tooluniverse-epigenomicsProduction-ready genomics and epigenomics data processing for BixBench questions
• tooluniverse-expression-data-retrievalRetrieves gene expression and omics datasets from ArrayExpress and BioStudies wi
• tooluniverse-gene-enrichmentPerform comprehensive gene enrichment and pathway analysis using gseapy (ORA and
• tooluniverse-gwas-drug-discoveryTransform GWAS signals into actionable drug targets and repurposing opportunitie
• tooluniverse-gwas-finemappingIdentify and prioritize causal variants at GWAS loci using statistical fine-mapp
• tooluniverse-gwas-snp-interpretationInterpret genetic variants (SNPs) from GWAS studies by aggregating evidence from
• tooluniverse-gwas-study-explorerCompare GWAS studies, perform meta-analyses, and assess replication across cohor
• tooluniverse-gwas-trait-to-geneDiscover genes associated with diseases and traits using GWAS data from the GWAS
• tooluniverse-image-analysisProduction-ready microscopy image analysis and quantitative imaging data skill f
• tooluniverse-immune-repertoire-analysisComprehensive immune repertoire analysis for T-cell and B-cell receptor sequenci
• tooluniverse-immunotherapy-response-predictionPredict patient response to immune checkpoint inhibitors (ICIs) using multi-biom
• tooluniverse-infectious-diseaseRapid pathogen characterization and drug repurposing analysis for infectious dis
• tooluniverse-literature-deep-researchConduct comprehensive literature research with target disambiguation, evidence g
• tooluniverse-metabolomicsComprehensive metabolomics research skill for identifying metabolites, analyzing
• tooluniverse-metabolomics-analysisAnalyze metabolomics data including metabolite identification, quantification, p
• tooluniverse-multi-omics-integrationIntegrate and analyze multiple omics datasets (transcriptomics, proteomics, epig
• tooluniverse-multiomic-disease-characterizationComprehensive multi-omics disease characterization integrating genomics, transcr
• tooluniverse-network-pharmacologyConstruct and analyze compound-target-disease networks for drug repurposing, pol
• tooluniverse-pharmacovigilanceAnalyze drug safety signals from FDA adverse event reports, label warnings, and
• tooluniverse-phylogeneticsProduction-ready phylogenetics and sequence analysis skill for alignment process
• tooluniverse-polygenic-risk-scoreBuild and interpret polygenic risk scores (PRS) for complex diseases using GWAS
• tooluniverse-precision-medicine-stratificationComprehensive patient stratification for precision medicine by integrating genom
• tooluniverse-precision-oncologyProvide actionable treatment recommendations for cancer patients based on molecu
• protein-interaction-network-analysisAnalyze protein-protein interaction networks using STRING, BioGRID, and SASBDB d
• tooluniverse-protein-structure-retrievalRetrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein
• tooluniverse-protein-therapeutic-designDesign novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided
• tooluniverse-proteomics-analysisAnalyze mass spectrometry proteomics data including protein quantification, diff
• tooluniverse-rare-disease-diagnosisProvide differential diagnosis for patients with suspected rare diseases based o
• tooluniverse-rnaseq-deseq2Production-ready RNA-seq differential expression analysis using PyDESeq2. Perfor
• tooluniverse-sequence-retrievalRetrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene d
• tooluniverse-single-cellProduction-ready single-cell and expression matrix analysis using scanpy, anndat
• tooluniverse-spatial-omics-analysisComputational analysis framework for spatial multi-omics data integration. Given
• tooluniverse-spatial-transcriptomicsAnalyze spatial transcriptomics data to map gene expression in tissue architectu
• tooluniverse-statistical-modelingPerform statistical modeling and regression analysis on biomedical datasets. Sup
• tooluniverse-structural-variant-analysisComprehensive structural variant (SV) analysis skill for clinical genomics. Clas
• tooluniverse-systems-biologyComprehensive systems biology and pathway analysis using multiple pathway databa
• tooluniverse-target-researchGather comprehensive biological target intelligence from 9 parallel research pat
• tooluniverse-variant-analysisProduction-ready VCF processing, variant annotation, mutation analysis, and stru
• tooluniverse-variant-interpretationSystematic clinical variant interpretation from raw variant calls to ACMG-classi
• torch-geometricGraph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GA
• torchdrugGraph-based drug discovery toolkit. Molecular property prediction (ADMET), prote
• torch-geometricGraph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GA
• tpd-ternary-complex-agent
• transformersThis skill should be used when working with pre-trained transformer models for n
• travel-health-analyzer分析旅行健康数据、评估目的地健康风险、提供疫苗接种建议、生成多语言紧急医疗信息卡片。支持WHO/CDC数据集成的专业级旅行健康风险评估。
• treatment-plansGenerate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format
• trial-eligibility-agent
• trialgpt-matching
• tumor-clonal-evolution-agent
• tumor-heterogeneity-agent
• tumor-mutational-burden-agent
• ukb-navigatorSemantic search across UK Biobank's 12,000+ data fields and publications — find
• umap-learnUMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visual
• uniprot-databaseDirect REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping
• universal-single-cell-annotator
• using-git-worktreesUse when starting feature work that needs isolation from current workspace or be
• using-superpowersUse when starting any conversation - establishes how to find and use skills, req
• usmlePrepare for US medical licensing exams with progress tracking, weak area analysi
• uspto-databaseAccess USPTO APIs for patent/trademark searches, examination history (PEDS), ass
• vaexUse this skill for processing and analyzing large tabular datasets (billions of
• varcadd-pathogenicity
• clinical-interpretation
• consensus-sequences
• deepvariant
• filtering-best-practices
• gatk-variant-calling
• joint-calling
• structural-variant-calling
• variant-annotation
• variant-calling
• variant-normalization
• vcf-basics
• vcf-manipulation
• vcf-statistics
• variant-interpretation-acmg
• varCADD
• vcf-annotatorAnnotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware
• verification-before-completionUse when about to claim work is complete, fixed, or passing, before committing o
• virtual-lab-agent
• wearable-analysis-agent
• weightloss-analyzer分析减肥数据、计算代谢率、追踪能量缺口、管理减肥阶段
• wellally-techIntegrate digital health data sources (Apple Health, Fitbit, Oura Ring) and conn
• wikipedia-searchSearch and fetch structured content from Wikipedia using the MediaWiki API for r
• writing-plansUse when you have a spec or requirements for a multi-step task, before touching
• writing-skillsUse when creating new skills, editing existing skills, or verifying skills work
• xlsxUse this skill any time a spreadsheet file is the primary input or output. This
• xlsxComprehensive spreadsheet creation, editing, and analysis with support for formu
• zarr-pythonChunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS in
• zinc-databaseAccess ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity