Skill OpenCode
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.
Skill OpenCode
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.
Skill OpenCode
Run remote BLAST searches against NCBI servers via Bio.Blast.NCBIWWW: pick the correct program and database, configure parameters (word size, composition-based statistics, hitlistsize), submit and poll the RID, then parse and interpret hits using Karlin-Altschul E-values and bit-scores. Avoids the maxtargetseqs misuse…
Skill OpenCode
Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources from repositories such as NCBI GEO/SRA, UniProt, Reactome, and PubMed.
Skill OpenCode
Cluster samples or features from bulk transcriptomics, proteomics, or metabolomics data.
Skill OpenCode
Reconstruct disease progression trajectories from longitudinal patient omics data.
Skill OpenCode
Infer differentiation trajectories, pseudotime ordering, RNA velocity, and cell fate probabilities from scRNA-seq data.
Skill OpenCode
Complete single-cell RNA-seq analysis using Scanpy from raw data to cell type annotation with clustering and visualization.
Skill OpenCode
Complete single-cell RNA-seq analysis using Seurat from raw data to cell type annotation with clustering and visualization.
Skill OpenCode
Advanced single-cell multi-omics analysis including scRNA-seq, scCITE-seq, scATAC-seq, and TARGET-seq. Use when analyzing single-cell data, cell type identification, trajectory analysis, differential expression, UMAP/clustering, integrating protein and RNA modalities (TotalVI), or working with Scanpy, Seurat…
Skill OpenCode
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation…
Skill OpenCode
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.
Skill OpenCode
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.
Skill OpenCode
scRNA-seq Explorer.
Skill OpenCode
Publication-quality visualizations for biomedical and genomics data. Use when creating volcano plots, heatmaps, UMAP plots, dot plots, survival curves, forest plots, or multi-panel figures. Includes scanpy, matplotlib, seaborn, plotly workflows with journal-ready aesthetics and proper statistical annotations.
Skill OpenCode
AI-driven integration of cellular imaging, laser microdissection, and ultra-sensitive mass spectrometry for spatially-resolved single-cell proteomics.
Skill OpenCode
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.
Skill OpenCode
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images. Use when processing tissue images for spatial transcriptomics.
Skill OpenCode
Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. Use when analyzing genomics data, searching for papers/datasets, or working with H5AD, CSV, GEO/SRA accessions, or biological data. Requires lobster-ai package…
Skill OpenCode
Next-generation sequencing data analysis pipelines including bulk RNA-seq, scRNA-seq preprocessing, variant calling, and quality control. Use when working with FASTQ files, alignment (STAR, BWA), quantification (featureCounts, Salmon), DESeq2/edgeR analysis, or building NGS pipelines. Supports GEO/SRA data retrieval.
Skill OpenCode
AI-powered RNA velocity analysis for predicting cellular state transitions, differentiation trajectories, and dynamic gene regulation from single-cell RNA sequencing data.
Skill OpenCode
Unified agent for leveraging single-cell foundation models (scGPT, scBERT, Geneformer, scFoundation) for cross-species annotation, perturbation prediction, and gene network inference.
Skill OpenCode
Execute the MAD-based single-cell RNA-seq QC workflow (scripts + Python API) to filter low-quality cells and emit reports plus filtered AnnData files.
Skill OpenCode
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: