experimental inferface from R to scvi-tools

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Documentation for package ‘scviR’ version 1.9.7

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

adtProfiles	produce a heatmap from a specialized CITE-seq SingleCellExperiment
anndataR	basic interface to anndata
bsklenv	python declarations
cacheCiteseq5k10kPbmcs	grab scvi-tools-processed PBMC CITE-seq data in anndata format (gzipped) from Open Storage Network
cacheCiteseq5k10kTutvae	grab scvi-tools VAE instance built on the PBMC datasets following the tutorial
cacheCiteseqHDPdata	retrieve and cache a 349-protein CITE-seq dataset as employed in scvi-tools tutorial
cacheCiteseqHDPmodel	grab scvi-tools muon-oriented VAE instance built on the PBMC datasets following the tutorial
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
exploreSubcl	app to explore diversity in RNA-subclusters within ADT clusters
getCh12AllSce	get list of cluster-specific SCE for 10k PBMC annotated as in OSCA book chapter 12
getCh12Sce	get SCE for 10k PBMC annotated as in OSCA book chapter 12
getCiteseq5k10kPbmcs	helper to get the processed anndata for CITE-seq PBMCs from scvi-tools tutorial
getCiteseqTutvae	helper to get the tutorial VAE for PBMCs from scvi-tools tutorial
getPro5k10kAdata	get an anndata reference to 5k10k protein after totalVI from tutorial
getSubclLM	get lmFit for heterogeneity across subclusters
getSubclusteringFeatures	get lmFit F-stat based collection of n genes most varying in mean across subclusters
getTotalVI5k10kAdata	get anndata reference to full totalVI processing of 5k10k data
getTotalVINormalized5k10k	get matrices of normalized quantifications from full totalVI 5k10k from tutorial
MuDataR	basic interface to MuData
muonR	basic interface to muon
pyHelp2	helper to get text from python help utility - may need handling through basilisk
scanpyHelper	shiny app that helps access documentation on python-accessible components
scanpyR	basic interface
scviHelper	shiny app that helps access documentation on python-accessible components
scviR	basic interface