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 May 2025, use BiocManager to install scviR in R 4.5.0 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 4.5.1 Patched (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] scviR_1.9.11                shiny_1.11.1               
##  [3] basilisk_1.21.5             reticulate_1.43.0          
##  [5] scater_1.37.0               ggplot2_4.0.0              
##  [7] scuttle_1.19.0              SingleCellExperiment_1.31.1
##  [9] SummarizedExperiment_1.39.2 Biobase_2.69.1             
## [11] GenomicRanges_1.61.5        Seqinfo_0.99.2             
## [13] IRanges_2.43.5              S4Vectors_0.47.4           
## [15] BiocGenerics_0.55.1         generics_0.1.4             
## [17] MatrixGenerics_1.21.0       matrixStats_1.5.0          
## [19] BiocStyle_2.37.1           
## 
## loaded via a namespace (and not attached):
##  [1] DBI_1.2.3            gridExtra_2.3        httr2_1.2.1         
##  [4] rlang_1.1.6          magrittr_2.0.4       compiler_4.5.1      
##  [7] RSQLite_2.4.3        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_2.9.0        
## [16] dbplyr_2.5.1         XVector_0.49.1       labeling_0.4.3      
## [19] promises_1.3.3       rmarkdown_2.30       ggbeeswarm_0.7.2    
## [22] tinytex_0.57         purrr_1.1.0          bit_4.6.0           
## [25] xfun_0.53            cachem_1.1.0         beachmat_2.25.5     
## [28] jsonlite_2.0.0       blob_1.2.4           later_1.4.4         
## [31] DelayedArray_0.35.3  BiocParallel_1.43.4  irlba_2.3.5.1       
## [34] parallel_4.5.1       R6_2.6.1             bslib_0.9.0         
## [37] RColorBrewer_1.1-3   limma_3.65.5         jquerylib_0.1.4     
## [40] Rcpp_1.1.0           bookdown_0.45        knitr_1.50          
## [43] splines_4.5.1        httpuv_1.6.16        Matrix_1.7-4        
## [46] tidyselect_1.2.1     dichromat_2.0-0.1    abind_1.4-8         
## [49] yaml_2.3.10          viridis_0.6.5        codetools_0.2-20    
## [52] curl_7.0.0           lattice_0.22-7       tibble_3.3.0        
## [55] withr_3.0.2          S7_0.2.0             evaluate_1.0.5      
## [58] BiocFileCache_2.99.6 pillar_1.11.1        BiocManager_1.30.26 
## [61] filelock_1.0.3       scales_1.4.0         xtable_1.8-4        
## [64] glue_1.8.0           pheatmap_1.0.13      tools_4.5.1         
## [67] BiocNeighbors_2.3.1  ScaledMatrix_1.17.0  cowplot_1.2.0       
## [70] grid_4.5.1           nlme_3.1-168         beeswarm_0.4.0      
## [73] BiocSingular_1.25.0  vipor_0.4.7          cli_3.6.5           
## [76] rsvd_1.0.5           rappdirs_0.3.3       S4Arrays_1.9.1      
## [79] viridisLite_0.4.2    dplyr_1.1.4          gtable_0.3.6        
## [82] sass_0.4.10          digest_0.6.37        SparseArray_1.9.1   
## [85] ggrepel_0.9.6        farver_2.1.2         memoise_2.0.1       
## [88] htmltools_0.5.8.1    lifecycle_1.0.4      statmod_1.5.0       
## [91] mime_0.13            bit64_4.6.0-1