omicverse

omicverse/omicverse

Skill Claude CodeCodex

BioContext knowledge: UniProt, AlphaFold, STRING, Reactome, GO, PanglaoDB, PubMed, OpenTargets queries via ov.biocontext for gene annotation.

omicverse/omicverse

Skill Claude CodeCodex

Bulk RNA-seq batch correction with pyComBat: remove batch effects from merged cohorts, export corrected matrices, and benchmark visualizations.

omicverse/omicverse

Skill Claude CodeCodex

Bulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, volcano plots, and pathway enrichment in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

PyDESeq2 differential expression: ID mapping, DE testing, fold-change thresholding, and GSEA enrichment visualization in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

STRING protein-protein interaction network analysis with pyPPI: query STRING database, build PPI graphs, expand with addnodes, and visualize styled networks for bulk gene lists.

omicverse/omicverse

Skill Claude CodeCodex

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.

omicverse/omicverse

Skill Claude CodeCodex

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.

omicverse/omicverse

Skill Claude CodeCodex

WGCNA co-expression network: soft-threshold, module detection, eigengenes, hub genes, and trait correlation in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

Export analysis results, data tables, and formatted spreadsheets to Excel files using openpyxl. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

omicverse/omicverse

Skill Claude CodeCodex

Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

omicverse/omicverse

Skill Claude CodeCodex

OmicVerse data I/O: use ov.read(), ov.io.readh5ad, read10xh5, read10xmtx, readvisium, readvisiumhd, readnanostring instead of scanpy. Covers h5ad, 10x, spatial, CSV formats.

omicverse/omicverse

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.).

omicverse/omicverse

Skill Claude CodeCodex

Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

omicverse/omicverse

Skill Claude CodeCodex

Publication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with ANY LLM provider.

omicverse/omicverse

Skill Claude CodeCodex

OmicVerse built-in datasets: pbmc3k, pancreas, dentategyrus, zebrafish, immune, spatial, multiome, plus createmockdataset() and predefinedsignatures GMT gene sets.

omicverse/omicverse

Skill Claude CodeCodex

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.

omicverse/omicverse

Skill Claude CodeCodex

Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

OmicVerse plotting: volcano, venn, boxplot, embedding, density, heatmap families, dotplot, convex hull, stacked bar, and Forbidden City color palettes.

omicverse/omicverse

Skill Claude CodeCodex

Cell type annotation: SCSA, MetaTiME, CellVote consensus, CellMatch, GPTAnno, weighted KNN label transfer in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

CellFateGenie: Adaptive Threshold Regression for pseudotime-associated gene discovery, Mellon density, lineage scoring via ov.single.Fate.

omicverse/omicverse

Skill Claude CodeCodex

CellPhoneDB v5 ligand-receptor analysis, CellChatViz plots, and the newer cccheatmap / cccnetworkplot / cccstatplot communication visualizations in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

Single-cell clustering (Leiden, Louvain, scICE, GMM), batch correction (Harmony, scVI, BBKNN, Combat), topic modeling, and cNMF in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

AUCell pathway scoring, metacell DEG, scDrug response, SCENIC regulons, cNMF programs, and NOCD community detection in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

Multi-omics integration: MOFA factor analysis, GLUE unpaired alignment, SIMBA batch correction, TOSICA label transfer, StaVIA trajectory. Covers scRNA+scATAC paired/unpaired workflows.