94 tagged single cell, measured the same way as everything else here.
Browse within: bioinformatics 89multi-omics 43knowledge-graph 42llm-agent 42multi-agents 42bulk-rna-seq 31omics 31transcriptomics 13deconvolution 11machine-learning 10python 10cell-communication 9bulkrna 8multi_omics 6
Skill Claude CodeCodex
Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
Skill Claude CodeCodex
Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
Skill Claude CodeCodex
Publication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with ANY LLM provider.
Skill Claude CodeCodex
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, and integrate with scanpy/PyTorch for population-scale single-cell analysis. Use this skill when: (1) Querying single-cell expression data by cell type, tissue, or disease, (2) Exploring available single-cell datasets…
Skill Claude CodeCodex
Use for any task involving the decoupler library — inferring biological activity/enrichment scores from omics data (bulk, single-cell, spatial). Triggers on estimating transcription factor (TF) activity, pathway activity, or gene-set enrichment from an AnnData/DataFrame; running ulm, mlm, ora, gsea, gsva, aucell…
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Discover and invoke 1,676 deduplicated biomedical AI agent skills from the Awesome Bio Agent Skills repository (20 source repos, 15 categories). Use this skill as a router whenever a user needs a bioinformatics/biomedical task (genomics, transcriptomics, single-cell, proteomics, protein design, clinical, epigenomics…
Skill Claude CodeCodex
Systematic workflow for clustering biological samples, features, or any quantitative data matrix. Implements multiple clustering algorithms with rigorous validation, comparison, and interpretation to identify meaningful data groupings.
Skill Claude CodeCodex
Core DESeq2 workflow for RNA-seq differential expression analysis with count data.
Skill Claude CodeCodex
Complete workflow for single-cell RNA-seq analysis using Seurat v5. Process raw data through quality control, normalization, clustering, and cell type annotation with publication-ready visualizations.
Skill Claude CodeCodex
Determine cell type composition at each spatial location through deconvolution or annotation. Use when user wants to know what cell types exist, their proportions, or where specific cells are located. Triggers: "cell type composition", "deconvolution", "what cells are here", "cell type proportions", "estimate cell…
Skill Claude CodeCodex
Find differentially expressed genes between conditions, regions, or cell types. Use when user wants to compare gene expression, find markers, or identify condition-specific changes. Triggers: "differential expression", "DEG", "marker genes", "compare conditions", "what genes differ", "find markers", "condition…
Skill Claude CodeCodex
Understand the biological meaning of gene sets through pathway and functional enrichment analysis. Use when user has gene lists (DEGs, markers, SVGs) and wants to know what pathways or functions they represent. Triggers: "pathway analysis", "enrichment", "GSEA", "GO terms", "what pathways", "biological function"…
Skill Claude CodeCodex
Single-cell cell-type annotation with evidence, conservative abstention, and reviewable drafts. Use this whenever the user wants to annotate, label, or identify cell types for pre-clustered single-cell or spatial transcriptomics data (.h5ad), or says things like "annotate my clusters", "what cell types are these?"…