omicverse/omicclaw
32 skills
$npx skills add omicverse/omicclawSkillInstalls
biocontext-knowledgeBioContext knowledge: UniProt, AlphaFold, STRING, Reactome, GO, PanglaoDB, PubMed, OpenTargets queries via ov.biocontext for gene annotation.bulk-combat-correctionBulk RNA-seq batch correction with pyComBat: remove batch effects from merged cohorts, export corrected matrices, and benchmark visualizations.bulk-deg-analysisBulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, volcano plots, and pathway enrichment in OmicVerse.bulk-deseq2-analysisPyDESeq2 differential expression: ID mapping, DE testing, fold-change thresholding, and GSEA enrichment visualization in OmicVerse.bulk-stringdb-ppiSTRING protein-protein interaction network analysis with pyPPI: query STRING database, build PPI graphs, expand with add_nodes, and visualize styled networks…bulk-to-single-deconvolutionTurn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and…bulk-trajblend-interpolationExtend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and…bulk-wgcna-analysisWGCNA co-expression network: soft-threshold, module detection, eigengenes, hub genes, and trait correlation in OmicVerse.data-export-excelExport analysis results, data tables, and formatted spreadsheets to Excel files using openpyxl. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).data-export-pdfCreate professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).data-io-loadingOmicVerse data I/O: use ov.read(), ov.io.read_h5ad, read_10x_h5, read_10x_mtx, read_visium, read_visium_hd, read_nanostring instead of scanpy.data-stats-analysisdata-transformdata-viz-plotsPublication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with ANY LLM provider.datasets-loadingOmicVerse built-in datasets: pbmc3k, pancreas, dentategyrus, zebrafish, immune, spatial, multiome, plus create_mock_dataset() and predefined_signatures GMT…fastq-analysisGuide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools…fm-foundation-modelsFoundation model workflows: scGPT, Geneformer, UCE, CellPLM cell embedding, annotation, integration via ov.fm unified API. 22 models.gsea-enrichmentGene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.plotting-visualizationOmicVerse plotting: volcano, venn, boxplot, embedding, density, dotplot, convex hull, stacked bar, and Forbidden City color palettes.single-annotationCell type annotation: SCSA, MetaTiME, CellVote consensus, CellMatch, GPTAnno, weighted KNN label transfer in OmicVerse.single-cellfate-analysisCellFateGenie: Adaptive Threshold Regression for pseudotime-associated gene discovery, Mellon density, lineage scoring via ov.single.Fate.single-cellphone-dbCellPhoneDB v5 ligand-receptor analysis, cell-cell communication networks, and CellChat-style visualization in OmicVerse.single-clusteringSingle-cell clustering (Leiden, Louvain, scICE, GMM), batch correction (Harmony, scVI, BBKNN, Combat), topic modeling, and cNMF in OmicVerse.single-downstream-analysisAUCell pathway scoring, metacell DEG, scDrug response, SCENIC regulons, cNMF programs, and NOCD community detection in OmicVerse.single-multiomicsMulti-omics integration: MOFA factor analysis, GLUE unpaired alignment, SIMBA batch correction, TOSICA label transfer, StaVIA trajectory.single-popv-annotationPopV population-level cell annotation: 10 algorithms (SCVI, SCANVI, CellTypist, OnClass, RF, SVM, XGBoost, BBKNN, HARMONY, SCANORAMA), consensus voting,…single-preprocessingSingle-cell QC, normalization, HVG detection, PCA, neighbor graph, UMAP/tSNE embedding pipelines in OmicVerse (CPU/GPU).single-scenic-grnSCENIC gene regulatory network: RegDiffusion GRN inference, cisTarget regulon pruning, AUCell scoring, RSS, regulon embeddings in OmicVerse.single-to-spatial-mappingMap scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker…single-trajectoryTrajectory & RNA velocity: PAGA, Palantir, VIA, dynamo, scVelo, latentvelo, graphvelo backends via ov.single.Velo. Pseudotime, stream plots.spatial-tutorialsSpatial transcriptomics: Visium/HD, Stereo-seq, Slide-seq preprocessing (crop, rotate, cellpose), deconvolution (Tangram, cell2location, Starfysh), clustering…tcga-preprocessingTCGA bulk RNA-seq preprocessing with pyTCGA: GDC sample sheets, expression archives, clinical metadata, Kaplan-Meier survival analysis, and annotated AnnData…