This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

scviR

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

experimental inferface from R to scvi-tools

Bioconductor version: Development (3.18)

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
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

Details

biocViews DataImport, Infrastructure, SingleCell, Software
Version 1.1.0
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
Linking To
Suggests knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle
System Requirements
Enhances
URL https://github.com/vjcitn/scviR
Bug Reports https://github.com/vjcitn/scviR/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scviR_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64) scviR_1.1.0.tgz
macOS Binary (arm64) scviR_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scviR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scviR
Bioc Package Browser https://code.bioconductor.org/browse/scviR/
Package Short Url https://bioconductor.org/packages/scviR/
Package Downloads Report Download Stats