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This is the development version of scviR; for the stable release version, see scviR.

experimental inferface from R to scvi-tools

Bioconductor version: Development (3.20)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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 HTML R Script
Reference Manual PDF


biocViews DataImport, Infrastructure, SingleCell, Software
Version 1.5.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 4.3), basilisk, shiny, SingleCellExperiment
Imports reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater, stats, MatrixGenerics
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Suggests knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package scviR_1.5.0.tar.gz
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macOS Binary (arm64) scviR_1.5.0.tgz
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Source Repository (Developer Access) git clone
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