Contents

1 Overview

scvi-tools is an element of the scverse 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:

2 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

3 Session information

sessionInfo()
## R version 4.5.0 Patched (2025-04-21 r88169)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] scviR_1.9.7                 shiny_1.10.0               
##  [3] basilisk_1.21.0             reticulate_1.42.0          
##  [5] scater_1.37.0               ggplot2_3.5.2              
##  [7] scuttle_1.19.0              SingleCellExperiment_1.31.0
##  [9] SummarizedExperiment_1.39.0 Biobase_2.69.0             
## [11] GenomicRanges_1.61.0        GenomeInfoDb_1.45.3        
## [13] IRanges_2.43.0              S4Vectors_0.47.0           
## [15] BiocGenerics_0.55.0         generics_0.1.3             
## [17] MatrixGenerics_1.21.0       matrixStats_1.5.0          
## [19] BiocStyle_2.37.0           
## 
## loaded via a namespace (and not attached):
##  [1] DBI_1.2.3             gridExtra_2.3         httr2_1.1.2          
##  [4] rlang_1.1.6           magrittr_2.0.3        compiler_4.5.0       
##  [7] RSQLite_2.3.11        mgcv_1.9-3            dir.expiry_1.17.0    
## [10] png_0.1-8             vctrs_0.6.5           pkgconfig_2.0.3      
## [13] crayon_1.5.3          fastmap_1.2.0         magick_2.8.6         
## [16] dbplyr_2.5.0          XVector_0.49.0        labeling_0.4.3       
## [19] promises_1.3.2        rmarkdown_2.29        UCSC.utils_1.5.0     
## [22] ggbeeswarm_0.7.2      tinytex_0.57          purrr_1.0.4          
## [25] bit_4.6.0             xfun_0.52             cachem_1.1.0         
## [28] beachmat_2.25.0       jsonlite_2.0.0        blob_1.2.4           
## [31] later_1.4.2           DelayedArray_0.35.1   BiocParallel_1.43.0  
## [34] irlba_2.3.5.1         parallel_4.5.0        R6_2.6.1             
## [37] bslib_0.9.0           RColorBrewer_1.1-3    limma_3.65.0         
## [40] jquerylib_0.1.4       Rcpp_1.0.14           bookdown_0.43        
## [43] knitr_1.50            splines_4.5.0         httpuv_1.6.16        
## [46] Matrix_1.7-3          tidyselect_1.2.1      dichromat_2.0-0.1    
## [49] abind_1.4-8           yaml_2.3.10           viridis_0.6.5        
## [52] codetools_0.2-20      curl_6.2.2            lattice_0.22-7       
## [55] tibble_3.2.1          basilisk.utils_1.21.0 withr_3.0.2          
## [58] evaluate_1.0.3        BiocFileCache_2.99.0  pillar_1.10.2        
## [61] BiocManager_1.30.25   filelock_1.0.3        scales_1.4.0         
## [64] xtable_1.8-4          glue_1.8.0            pheatmap_1.0.12      
## [67] tools_4.5.0           BiocNeighbors_2.3.0   ScaledMatrix_1.17.0  
## [70] cowplot_1.1.3         grid_4.5.0            nlme_3.1-168         
## [73] beeswarm_0.4.0        BiocSingular_1.25.0   vipor_0.4.7          
## [76] cli_3.6.5             rsvd_1.0.5            rappdirs_0.3.3       
## [79] S4Arrays_1.9.0        viridisLite_0.4.2     dplyr_1.1.4          
## [82] gtable_0.3.6          sass_0.4.10           digest_0.6.37        
## [85] SparseArray_1.9.0     ggrepel_0.9.6         farver_2.1.2         
## [88] memoise_2.0.1         htmltools_0.5.8.1     lifecycle_1.0.4      
## [91] httr_1.4.7            statmod_1.5.0         mime_0.13            
## [94] bit64_4.6.0-1