omicverse

omicverse/omicverse

Skill Claude CodeCodex

PopV population-level cell annotation: 10 algorithms (SCVI, SCANVI, CellTypist, OnClass, RF, SVM, XGBoost, BBKNN, HARMONY, SCANORAMA), consensus voting, pretrained hub models.

omicverse/omicverse

Skill Claude CodeCodex

Single-cell QC, normalization, HVG detection, PCA, neighbor graph, UMAP/tSNE embedding pipelines in OmicVerse (CPU/GPU).

omicverse/omicverse

Skill Claude CodeCodex

SCENIC gene regulatory network: RegDiffusion GRN inference, cisTarget regulon pruning, AUCell scoring, RSS, regulon embeddings in OmicVerse.

omicverse/omicverse

Skill Claude CodeCodex

Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.

omicverse/omicverse

Skill Claude CodeCodex

Trajectory & RNA velocity: PAGA, Palantir, VIA, dynamo, scVelo, latentvelo, graphvelo backends via ov.single.Velo. Pseudotime, stream plots.

omicverse/omicverse

Skill Claude CodeCodex

Spatial transcriptomics: Visium/HD, Stereo-seq, Slide-seq preprocessing (crop, rotate, cellpose), deconvolution (Tangram, cell2location, Starfysh), clustering (GraphST, STAGATE), integration, trajectory, communication.

omicverse/omicverse

Skill Claude CodeCodex

TCGA bulk RNA-seq preprocessing with pyTCGA: GDC sample sheets, expression archives, clinical metadata, Kaplan-Meier survival analysis, and annotated AnnData export.

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

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/omicclaw

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/omicclaw

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/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

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/omicclaw

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/omicclaw

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/omicclaw

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/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

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/omicclaw

Skill Claude CodeCodex

Foundation model workflows: scGPT, Geneformer, UCE, CellPLM cell embedding, annotation, integration via ov.fm unified API. 22 models.