Function reference • scviR

All functions
`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
`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
`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

Reference

All functions