Package: scviR 1.12.0

Vincent Carey

scviR: experimental inferface from R to scvi-tools

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.

Authors:Vincent Carey [aut, cre]

scviR_1.12.0.tar.gz
scviR_1.12.0.zip(r-4.7)scviR_1.12.0.zip(r-4.6)scviR_1.12.0.zip(r-4.5)
scviR_1.12.0.tgz(r-4.6-any)scviR_1.12.0.tgz(r-4.5-any)
scviR_1.12.0.tar.gz(r-4.7-any)scviR_1.12.0.tar.gz(r-4.6-any)
scviR_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scviR/json (API)

# Install 'scviR' in R:
install.packages('scviR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vjcitn/scvir/issues

Datasets:
  • clusters.adt - ADT-based cluster labels for 7472 cells in OSCA chapter 12 analysis
  • clusters.rna - MRNA-based cluster labels for 7472 cells in OSCA chapter 12 analysis

On CRAN:

Conda:

infrastructuresinglecelldataimportbioconductorcite-seqczieoss6-biocgpuscverse

4.92 score 7 stars 12 scripts 248 downloads 23 exports 130 dependencies

Last updated from:574204bec6 (on RELEASE_3_23). Checks:6 ERROR, 2 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR209
linux-devel-x86_64NOTE469
source / vignettesOK1023
linux-release-x86_64NOTE416
macos-release-arm64ERROR509
macos-oldrel-arm64ERROR429
windows-develERROR347
windows-releaseERROR381
windows-oldrelERROR327
wasm-releaseOK166

Exports:adtProfilesanndataRcacheCiteseq5k10kPbmcscacheCiteseq5k10kTutvaecacheCiteseqHDPdatacacheCiteseqHDPmodelexploreSubclgetCh12AllScegetCh12ScegetCiteseq5k10kPbmcsgetCiteseqTutvaegetPro5k10kAdatagetSubclLMgetSubclusteringFeaturesgetTotalVI5k10kAdatagetTotalVINormalized5k10kMuDataRmuonRpyHelp2scanpyHelperscanpyRscviHelperscviR

Dependencies:abindaskpassassortheadbase64encbasiliskbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiocSingularbitbit64blobbslibcachemCairoclicodetoolscommonmarkcpp11curlDBIdbplyrDelayedArraydigestdir.expirydplyrdqrngfarverfastmapfilelockFNNfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtableherehtmltoolshttpuvhttr2IRangesirlbaisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpheatmappillarpkgconfigpngpromisespurrrR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRcppTOMLreticulaterlangrprojrootRSpectraRSQLitersvdRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscuttleSeqinfoshinySingleCellExperimentsitmosnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectutf8uwotvctrsviporviridisviridisLitewithrxtableXVector

CITE-seq setup for scviR, 2025

Vince Carey stvjc at channing.harvard.edu

Rendered fromnew_citeseq.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-10-21
Started: 2025-05-12

Comparing totalVI and OSCA book CITE-seq analyses

OSCA book authors and Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromcompch12.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-05-12
Started: 2023-02-17

scvi-tools CITE-seq tutorial in R, using serialized tutorial components

Follows scvi-tools doc, Gayoso, Steier et al. DOI 10.1038/s41592-020-01050-x

Rendered fromciteseq_tut.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-05-12
Started: 2023-02-05

scviR: an R package interfacing Bioconductor and scvi-tools

Vince Carey stvjc at channing.harvard.edu

Rendered fromscviR.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-05-12
Started: 2023-01-26

Readme and manuals

Help Manual

Help pageTopics
produce a heatmap from a specialized CITE-seq SingleCellExperimentadtProfiles
basic interface to anndataanndataR
python declarationsbsklenv
grab scvi-tools-processed PBMC CITE-seq data in anndata format (gzipped) from Open Storage NetworkcacheCiteseq5k10kPbmcs
Deprecated: grab scvi-tools VAE instance built on the PBMC datasets following the tutorialcacheCiteseq5k10kTutvae
retrieve and cache a 349-protein CITE-seq dataset as employed in scvi-tools tutorialcacheCiteseqHDPdata
grab scvi-tools muon-oriented VAE instance built on the PBMC datasets following the tutorialcacheCiteseqHDPmodel
ADT-based cluster labels for 7472 cells in OSCA chapter 12 analysisclusters.adt
mRNA-based cluster labels for 7472 cells in OSCA chapter 12 analysisclusters.rna
app to explore diversity in RNA-subclusters within ADT clustersexploreSubcl
get list of cluster-specific SCE for 10k PBMC annotated as in OSCA book chapter 12getCh12AllSce
get SCE for 10k PBMC annotated as in OSCA book chapter 12getCh12Sce
helper to get the processed anndata for CITE-seq PBMCs from scvi-tools tutorialgetCiteseq5k10kPbmcs
helper to get the tutorial VAE for PBMCs from scvi-tools tutorialgetCiteseqTutvae
get an anndata reference to 5k10k protein after totalVI from tutorialgetPro5k10kAdata
get lmFit for heterogeneity across subclustersgetSubclLM
get lmFit F-stat based collection of n genes most varying in mean across subclustersgetSubclusteringFeatures
get anndata reference to full totalVI processing of 5k10k datagetTotalVI5k10kAdata
get matrices of normalized quantifications from full totalVI 5k10k from tutorialgetTotalVINormalized5k10k
basic interface to MuDataMuDataR
basic interface to muonmuonR
helper to get text from python help utility - may need handling through basiliskpyHelp2
shiny app that helps access documentation on python-accessible componentsscanpyHelper
basic interfacescanpyR
shiny app that helps access documentation on python-accessible componentsscviHelper
basic interfacescviR