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totalVI and MultiVI — deep generative models from scvi-tools for multi-modal single-cell integration. totalVI jointly models scRNA-seq and protein (CITE-seq) data via a variational autoencoder for den
Use with AI
Install the MCP server or CLI to instantly fetch totalVI / MultiVI documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/totalvimultivi
Muon — multimodal omics data analysis framework from the scverse ecosystem. Built on the MuData container for multi-modal single-cell experiments including CITE-seq, Multiome (RNA+ATAC), TEA-seq, and
2 shared topics • 1 shared operation
Use when working with SATURN for cross-species single-cell RNA-seq integration that combines AnnData count matrices with protein embedding TorchDicts. SATURN trains macrogene representations with k-me
2 shared topics • 1 shared operation
Use when working with scMoMaT, single-cell mosaic integration, multi-omics matrix tri-factorization, or marker discovery across RNA, ATAC, and protein batches with missing modalities. scMoMaT integrat
2 shared topics • 1 shared operation
salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s
1 shared topic • 2 shared operations
Salmon is an ultrafast, bias-correcting tool for quantifying transcript abundances from RNA-seq reads using quasi-mapping or selective alignment. Alevin is Salmon's single-cell mode for generating cel
1 shared topic • 2 shared operations