DOI: 10.18129/B9.bioc.scviR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scviR.

experimental inferface from R to scvi-tools

Bioconductor version: 3.17

This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

Author: Vincent Carey [aut, cre]

Maintainer: Vincent Carey <stvjc at>

Citation (from within R, enter citation("scviR")):


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HTML R Script Comparing totalVI and OSCA book CITE-seq analyses
HTML R Script scvi-tools CITE-seq tutorial in R, using serialized tutorial components
HTML R Script scviR: an R package interfacing Bioconductor and scvi-tools
PDF   Reference Manual


biocViews DataImport, Infrastructure, SingleCell, Software
Version 1.0.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License Artistic-2.0
Depends R (>= 4.3), basilisk, shiny, SingleCellExperiment
Imports reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater
Suggests knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle
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