omicverse/omicverse-skills

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omicverse-single-cell-via-trajectory VIA (Stassen 2021) single-cell trajectory inference via `omicverse.single.pyVIA` - PARC-clustering + lazy-teleporting…

omicverse/omicverse-skills

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omicverse-visualization-for-bulk-color-systems-and-single-cell-d OmicVerse plotting: volcano, venn, boxplot, embedding, density, dotplot, convex hull, stacked bar, and Forbidden City…

omicverse/omicverse-skills

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single-cell-downstream-analysis AUCell pathway scoring, metacell DEG, scDrug response, SCENIC regulons, cNMF programs, and NOCD community detection i…

omicverse/omicverse-skills

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single-cell-multi-omics-integration Multi-omics integration: MOFA factor analysis, GLUE unpaired alignment, SIMBA batch correction, TOSICA label transfer…

omicverse/omicverse-skills

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single-popv-annotation PopV population-level cell annotation: 10 algorithms (SCVI, SCANVI, CellTypist, OnClass, RF, SVM, XGBoost, BBKNN, HAR…

omicverse/omicverse-skills

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single2spatial-spatial-mapping Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest t…

omicverse/omicverse-skills

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spatial-transcriptomics-tutorials-with-omicverse Spatial transcriptomics: Visium/HD, Stereo-seq, Slide-seq preprocessing (crop, rotate, cellpose), deconvolution (Tang…

omicverse/omicverse-skills

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string-protein-interaction-analysis-with-omicverse STRING protein-protein interaction network analysis with pyPPI: query STRING database, build PPI graphs, expand with …

omicverse/omicverse-skills

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tcga-bulk-data-preprocessing-with-omicverse TCGA bulk RNA-seq preprocessing with pyTCGA: GDC sample sheets, expression archives, clinical metadata, Kaplan-Meier …

omicverse/omicverse-skills

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