Skill Claude CodeCodex
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
not rated 1.1k
+1 5mo ago B 35 tokens
1.1kStars on the repository
200Mods indexed here, across every type
5mo agoLast push, which is what freshness is scored on
noneNo LICENSE: all rights reserved, so bodies are not copied
Skill Claude CodeCodex
Generates short, imperative guidance prompts for the next experimental step from current video frame and protocol context. Output is optimized for voice broadcast (TTS) or AR overlay — concise, actionable, command-style — to guide researchers in real time, correct deviations, or resume experiments without breaking…
not rated 1.1k
+1 5mo ago A 66 tokens
Skill Claude CodeCodex
Converts natural language or PDF protocol text into executable step sequences for Opentrons or PyLabRobot. Parses protocol descriptions to extract pipette volumes, well positions, temperatures, incubation times, and transfer patterns; outputs Python code snippets or JSON instruction lists ready for robot execution or…
not rated 1.1k
+1 5mo ago A 62 tokens
scanpy
52Skill Claude CodeCodex
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…
not rated 1.1k
+1 5mo ago A 68 tokens
scikit-bio
53Skill Claude CodeCodex
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
not rated 1.1k
+1 5mo ago A 54 tokens
Skill Claude CodeCodex
Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions…
not rated 1.1k
+1 5mo ago A 91 tokens
scvi-tools
55Skill Claude CodeCodex
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
not rated 1.1k
+1 5mo ago A 65 tokens
Skill Claude CodeCodex
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
not rated 1.1k
+1 5mo ago A 44 tokens
Skill Claude CodeCodex
Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic lethal interactions, and drug targets. Perform sgRNA count processing, gene-level scoring (MAGeCK, BAGEL), quality control, pathway…
not rated 1.1k
+1 5mo ago A 112 tokens
Skill Claude CodeCodex
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility…
not rated 1.1k
+1 5mo ago A 205 tokens
Skill Claude CodeCodex
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention…
not rated 1.1k
+1 5mo ago A 88 tokens
Skill Claude CodeCodex
Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supports GO enrichment (BP, MF, CC), KEGG, Reactome, WikiPathways, MSigDB Hallmark, and 220+ Enrichr libraries. Handles multiple ID types (gene symbols, Ensembl, Entrez…
not rated 1.1k
+1 5mo ago A 160 tokens
Skill Claude CodeCodex
Transform GWAS signals into actionable drug targets and repurposing opportunities. Performs locus-to-gene mapping, target druggability assessment, existing drug identification, safety profile evaluation, and clinical trial matching. Use when discovering drug targets from GWAS data, finding drug repurposing…
not rated 1.1k
+1 5mo ago A 79 tokens
Skill Claude CodeCodex
Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities for causal variants, links variants to genes via L2G predictions, annotates functional consequences, and suggests validation strategies. Use when asked to fine-map GWAS…
not rated 1.1k
+1 5mo ago A 84 tokens
Skill Claude CodeCodex
Interpret genetic variants (SNPs) from GWAS studies by aggregating evidence from multiple databases (GWAS Catalog, Open Targets Genetics, ClinVar). Retrieves variant annotations, GWAS trait associations, fine-mapping evidence, locus-to-gene predictions, and clinical significance. Use when asked to interpret a SNP by…
not rated 1.1k
+1 5mo ago A 110 tokens
Skill Claude CodeCodex
Compare GWAS studies, perform meta-analyses, and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog and Open Targets Genetics to compare study designs, effect sizes, ancestry diversity, and heterogeneity statistics. Use when comparing GWAS studies for a trait, performing meta-analysis of genetic…
not rated 1.1k
+1 5mo ago A 88 tokens
Skill Claude CodeCodex
Discover genes associated with diseases and traits using GWAS data from the GWAS Catalog (500,000+ associations) and Open Targets Genetics (L2G predictions). Identifies genetic risk factors, prioritizes causal genes via locus-to-gene scoring, and assesses druggability. Use when asked to find genes associated with a…
not rated 1.1k
+1 5mo ago A 108 tokens
Skill Claude CodeCodex
Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3 characteristics, convergence, and predict epitope specificity. Integrate with single-cell data for clonotype-phenotype associations. Use for…
not rated 1.1k
+1 5mo ago A 103 tokens
Skill Claude CodeCodex
Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Processes LC-MS, GC-MS, NMR data from targeted and untargeted experiments. Performs normalization, statistical analysis, pathway enrichment, metabolite-enzyme integration, and biomarker discovery. Use…
not rated 1.1k
+1 5mo ago A 113 tokens
Skill Claude CodeCodex
Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve…
not rated 1.1k
+1 5mo ago A 108 tokens
Skill Claude CodeCodex
Integrate and analyze multiple omics datasets (transcriptomics, proteomics, epigenomics, genomics, metabolomics) for systems biology and precision medicine. Performs cross-omics correlation, multi-omics clustering (MOFA+, NMF), pathway-level integration, and sample matching. Coordinates ToolUniverse skills for…
not rated 1.1k
+1 5mo ago A 161 tokens
Skill Claude CodeCodex
Comprehensive multi-omics disease characterization integrating genomics, transcriptomics, proteomics, pathway, and therapeutic layers for systems-level understanding. Produces a detailed multi-omics report with quantitative confidence scoring (0-100), cross-layer gene concordance analysis, biomarker candidates…
not rated 1.1k
+1 5mo ago A 118 tokens
Skill Claude CodeCodex
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness/RCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and…
not rated 1.1k
+1 5mo ago A 177 tokens
Skill Claude CodeCodex
Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles, interprets PRS percentiles, and assesses disease predisposition across conditions including type 2 diabetes, coronary artery disease, and Alzheimer's disease. Use when asked to…
not rated 1.1k
+1 5mo ago A 101 tokens
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