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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| CITE-seq setup for scviR, 2025 | 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 | 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 |
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 |