---
title: "scviR: an R package interfacing Bioconductor and scvi-tools"
author: "Vince Carey stvjc at channing.harvard.edu"
date: "`r format(Sys.time(), '%B %d, %Y')`"
vignette: >
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{scviR: an R package interfacing Bioconductor and scvi-tools}
  %\VignetteEncoding{UTF-8}
output:
  BiocStyle::html_document:
    highlight: pygments
    number_sections: yes
    theme: united
    toc: yes
---

# Overview

[scvi-tools](https://scvi-tools.org/) is
an element of the [scverse](https://scverse.org/) toolchest for
single-cell omics data analysis.

The scviR package is a very elementary approach to interfacing
between R, Bioconductor and scvi-tools.  The long-term plan is to
illustrate several aspects of variational inference (VI) applied to single
cell genomics in a way
that is convenient for Bioconductor users.

The package makes use of SingleCellExperiment and anndata
representations of single-cell genomic assays.

Several points should be kept in mind when using this package:

- scvi-tools components develop rapidly; we are
using [basilisk](https://bioconductor.org/packages/basilisk)
to manage R/python interoperation, and as of current
writing we work with version 0.20.0 of scvi-tools.  Specific
versions of python components are enumerated in the file R/basilisk.R.
- A docker container based on a PyTorch-oriented image in
the [NVIDIA container registry](nvcr.io/nvidia/pytorch:22.12-py3) includes
R 4.2.2 and sufficient python 3 infrastructure to use scvi-tools 0.20.0
and scviR 0.0.2.  A Dockerfile is in scviR/inst/Docker;
`vjcitn/nvidpt_bioc:0.0.2` can be pulled from dockerhub, it reports
size 26.5GB.  Container resources will be updated as needed.  Users
should file issues at the package GitHub [repo](https://github.com/vjcitn/scviR)
if the container is stale.
- Code presented in the cite-seq tutorial
vignette follows [the colab notebook
for scvi-tools 0.18.0](https://colab.research.google.com/github/scverse/scvi-tutorials/blob/0.18.0/totalVI.ipynb).  *We will check for modifications in the scvi-tools 0.20.0 notebook*.
- Additional work on this package will facilitate comparisons between
outcomes of Bioconductor, scVI, and other VI-oriented analytic toolkits in the
single-cell domain.

# Installation and use

As of Feb 2023, use BiocManager to install scviR in R 4.2.2 or above:
```
BiocManager::install("vjcitn/scviR")
```
Be sure the `remotes` package has been installed.  If you are working at a slow
internet connection, it may be useful to set `options(timeout=3600)` when running 
functions 

- `getCh12AllSce()` (74 MB will be retrieved and cached)
- `getCh12Sce()` (58 MB will be retrieved and cached)
- `getCiteseqTutvae()` (1.2 GB will be retrieved and cached)
- `getTotalVINormalized5k10k()` (191 MB will be retrieved and cached)


# Session information

```{r lksess}
sessionInfo()
```