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Bioconductor - scviR

scviR

This is the released version of scviR; for the devel version, see scviR.

experimental inferface from R to scvi-tools

Bioconductor version: Release (3.21)

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] ORCID: 0000-0003-4046-0063

Maintainer: Vincent Carey <stvjc at channing.harvard.edu>

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

To install this package, start R (version "4.5") 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")

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 1.8.0 In Bioconductor since BioC 3.17 (R-4.3) (2 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 Package Archives

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

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