scviR
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see scviR.
experimental inferface from R to scvi-tools
Bioconductor version: Release (3.23)
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 channing.harvard.edu>
citation("scviR")):Vincent Carey. scviR: experimental inferface from R to scvi-tools. doi:10.18129/B9.bioc.scviR, R package version 1.12.0, https://bioconductor.org/packages/scviR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scviR")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scviR")| scvi-tools CITE-seq tutorial in R, using serialized tutorial components | HTML | R Script |
| Comparing totalVI and OSCA book CITE-seq analyses | HTML | R Script |
| CITE-seq setup for scviR, 2025 | HTML | R Script |
| scviR: an R package interfacing Bioconductor and scvi-tools | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataImport, Infrastructure, SingleCell, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3), basilisk, shiny, SingleCellExperiment |
| Imports | reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater, stats, MatrixGenerics |
| System Requirements | |
| URL | https://github.com/vjcitn/scviR |
| Bug Reports | https://github.com/vjcitn/scviR/issues |
See More
| Suggests | knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scviR_1.12.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | scviR_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | scviR_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scviR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scviR |
| Package Short Url | https://bioconductor.org/packages/scviR/ |
| Package Downloads Report | Download Stats |