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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 (3.19)

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 "4.4") 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 1.3.1
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
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
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Package Archives

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

Source Package scviR_1.3.1.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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