scviR
This is thereleased version of scviR; for the devel version, seescviR.
experimental inferface from R to scvi-tools
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | 1.10.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (2.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | scviR_1.10.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |