Individual skill

multimodal-omics-integration

Multimodal and multi-section integration for spatial and single-cell omics: totalVI joint RNA + protein (Visium CytAssist Gene and Protein, CITE-seq), MultiVI joint RNA + ATAC (10x Multiome, spatial ATAC-RNA), BBKNN integration of several tissue sections, scanpy ingest label transfer between sections, and gene signature scores mapped on tissue. Outputs joint latent spaces, denoised protein maps, integrated clusters, transferred labels. For dissociated CITE-seq and scVI/scANVI use scvi-tools-single-cell; for MOFA+ factor analysis use mofaplus-multi-omics or muon-multiomics-singlecell; for Harmony use harmony-batch-correction.

skills/genomics-bioinformatics/spatial-transcriptomics/multimodal-omics-integration/SKILL.md

Source commit 55c1bd3e863d11bf5a853d24bcdda10c88e6eddf

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Nov 5, 2026

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