Skill Claude CodeCodex
BioContext knowledge: UniProt, AlphaFold, STRING, Reactome, GO, PanglaoDB, PubMed, OpenTargets queries via ov.biocontext for gene annotation.
33 3mo ago A 45 tokens
GPL-3.0
33Stars on the repository
32Mods indexed here, across every type
3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.).
33 3mo 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.).
33 3mo 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.
33 3mo 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.).
33 3mo 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.).
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo 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.
33 3mo ago A 41 tokens
GPL-3.0