omicverse

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

CellPhoneDB v5 ligand-receptor analysis, cell-cell communication networks, and CellChat-style visualization in OmicVerse.

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

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.

omicverse/omicclaw

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/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

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/omicclaw

Skill Claude CodeCodex

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

omicverse/omicclaw

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/omicclaw

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.