scviR

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 channing.harvard.edu>

Installation

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

 

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

Details

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
LinkingTo
Suggests	knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/vjcitn/scviR
BugReports	https://github.com/vjcitn/scviR/issues
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_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64)	scviR_1.0.0.tgz
macOS Binary (arm64)	scviR_1.0.0.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