Skill Claude CodeCodex
BioContext knowledge: UniProt, AlphaFold, STRING, Reactome, GO, PanglaoDB, PubMed, OpenTargets queries via ov.biocontext for gene annotation.
not rated 33 5mo ago A 45 tokens
GPL-3.0
33Stars on the repository
32Mods indexed here, across every type
5mo agoLast push, which is what freshness is scored on
GPL-3.0Licence, which decides whether bodies are shown
Skill Claude CodeCodex
Bulk RNA-seq batch correction with pyComBat: remove batch effects from merged cohorts, export corrected matrices, and benchmark visualizations.
not rated 33 5mo ago A 40 tokens
GPL-3.0
Skill Claude CodeCodex
Bulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, volcano plots, and pathway enrichment in OmicVerse.
not rated 33 5mo ago A 44 tokens
GPL-3.0
Skill Claude CodeCodex
PyDESeq2 differential expression: ID mapping, DE testing, fold-change thresholding, and GSEA enrichment visualization in OmicVerse.
not rated 33 5mo ago A 43 tokens
GPL-3.0
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.
not rated 33 5mo ago A 46 tokens
GPL-3.0
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.
not rated 33 5mo ago A 55 tokens
GPL-3.0
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.
not rated 33 5mo ago A 46 tokens
GPL-3.0
Skill Claude CodeCodex
WGCNA co-expression network: soft-threshold, module detection, eigengenes, hub genes, and trait correlation in OmicVerse.
not rated 33 5mo ago A 39 tokens
GPL-3.0
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.).
not rated 33 5mo ago A 38 tokens
GPL-3.0
Skill Claude CodeCodex
Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
not rated 33 5mo ago A 36 tokens
GPL-3.0
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.
not rated 33 5mo ago A 68 tokens
GPL-3.0
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.).
not rated 33 5mo ago A 40 tokens
GPL-3.0
Skill Claude CodeCodex
Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
not rated 33 5mo ago A 32 tokens
GPL-3.0
Skill Claude CodeCodex
Publication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with ANY LLM provider.
not rated 33 5mo ago A 36 tokens
GPL-3.0
Skill Claude CodeCodex
OmicVerse built-in datasets: pbmc3k, pancreas, dentategyrus, zebrafish, immune, spatial, multiome, plus createmockdataset() and predefinedsignatures GMT gene sets.
not rated 33 5mo ago A 45 tokens
GPL-3.0
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.
not rated 33 5mo ago A 51 tokens
GPL-3.0
Skill Claude CodeCodex
Foundation model workflows: scGPT, Geneformer, UCE, CellPLM cell embedding, annotation, integration via ov.fm unified API. 22 models.
not rated 33 5mo ago A 36 tokens
GPL-3.0
Skill Claude CodeCodex
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
not rated 33 5mo ago A 31 tokens
GPL-3.0
Skill Claude CodeCodex
OmicVerse plotting: volcano, venn, boxplot, embedding, density, dotplot, convex hull, stacked bar, and Forbidden City color palettes.
not rated 33 5mo ago A 47 tokens
GPL-3.0
Skill Claude CodeCodex
Cell type annotation: SCSA, MetaTiME, CellVote consensus, CellMatch, GPTAnno, weighted KNN label transfer in OmicVerse.
not rated 33 5mo ago A 42 tokens
GPL-3.0
Skill Claude CodeCodex
CellFateGenie: Adaptive Threshold Regression for pseudotime-associated gene discovery, Mellon density, lineage scoring via ov.single.Fate.
not rated 33 5mo ago A 39 tokens
GPL-3.0
Skill Claude CodeCodex
CellPhoneDB v5 ligand-receptor analysis, cell-cell communication networks, and CellChat-style visualization in OmicVerse.
not rated 33 5mo ago A 36 tokens
GPL-3.0
Skill Claude CodeCodex
Single-cell clustering (Leiden, Louvain, scICE, GMM), batch correction (Harmony, scVI, BBKNN, Combat), topic modeling, and cNMF in OmicVerse.
not rated 33 5mo ago A 56 tokens
GPL-3.0
Skill Claude CodeCodex
AUCell pathway scoring, metacell DEG, scDrug response, SCENIC regulons, cNMF programs, and NOCD community detection in OmicVerse.
not rated 33 5mo ago A 41 tokens
GPL-3.0
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: