# experimental inferface from R to scvi-tools

## Documentation for package ‘scviR’ version 1.0.0

- 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
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