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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [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] scater_1.32.0               scuttle_1.14.0             
##  [3] reshape2_1.4.4              ggplot2_3.5.1              
##  [5] scviR_1.4.0                 SingleCellExperiment_1.26.0
##  [7] SummarizedExperiment_1.34.0 Biobase_2.64.0             
##  [9] GenomicRanges_1.56.0        GenomeInfoDb_1.40.0        
## [11] IRanges_2.38.0              S4Vectors_0.42.0           
## [13] BiocGenerics_0.50.0         MatrixGenerics_1.16.0      
## [15] matrixStats_1.3.0           shiny_1.8.1.1              
## [17] basilisk_1.16.0             reticulate_1.36.1          
## [19] BiocStyle_2.32.0           
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.2                 gridExtra_2.3            
##   [3] rlang_1.1.3               magrittr_2.0.3           
##   [5] compiler_4.4.0            RSQLite_2.3.6            
##   [7] mgcv_1.9-1                dir.expiry_1.12.0        
##   [9] DelayedMatrixStats_1.26.0 png_0.1-8                
##  [11] vctrs_0.6.5               stringr_1.5.1            
##  [13] pkgconfig_2.0.3           crayon_1.5.2             
##  [15] fastmap_1.1.1             magick_2.8.3             
##  [17] dbplyr_2.5.0              XVector_0.44.0           
##  [19] labeling_0.4.3            utf8_1.2.4               
##  [21] promises_1.3.0            rmarkdown_2.26           
##  [23] UCSC.utils_1.0.0          ggbeeswarm_0.7.2         
##  [25] tinytex_0.50              purrr_1.0.2              
##  [27] bit_4.0.5                 xfun_0.43                
##  [29] zlibbioc_1.50.0           cachem_1.0.8             
##  [31] beachmat_2.20.0           jsonlite_1.8.8           
##  [33] blob_1.2.4                highr_0.10               
##  [35] later_1.3.2               DelayedArray_0.30.0      
##  [37] BiocParallel_1.38.0       irlba_2.3.5.1            
##  [39] parallel_4.4.0            R6_2.5.1                 
##  [41] stringi_1.8.3             bslib_0.7.0              
##  [43] RColorBrewer_1.1-3        limma_3.60.0             
##  [45] jquerylib_0.1.4           Rcpp_1.0.12              
##  [47] bookdown_0.39             knitr_1.46               
##  [49] splines_4.4.0             httpuv_1.6.15            
##  [51] Matrix_1.7-0              tidyselect_1.2.1         
##  [53] abind_1.4-5               yaml_2.3.8               
##  [55] viridis_0.6.5             codetools_0.2-20         
##  [57] curl_5.2.1                plyr_1.8.9               
##  [59] lattice_0.22-6            tibble_3.2.1             
##  [61] withr_3.0.0               basilisk.utils_1.16.0    
##  [63] evaluate_0.23             BiocFileCache_2.12.0     
##  [65] pillar_1.9.0              BiocManager_1.30.22      
##  [67] filelock_1.0.3            generics_0.1.3           
##  [69] sparseMatrixStats_1.16.0  munsell_0.5.1            
##  [71] scales_1.3.0              xtable_1.8-4             
##  [73] glue_1.7.0                pheatmap_1.0.12          
##  [75] tools_4.4.0               BiocNeighbors_1.22.0     
##  [77] ScaledMatrix_1.12.0       cowplot_1.1.3            
##  [79] grid_4.4.0                colorspace_2.1-0         
##  [81] nlme_3.1-164              GenomeInfoDbData_1.2.12  
##  [83] beeswarm_0.4.0            BiocSingular_1.20.0      
##  [85] vipor_0.4.7               cli_3.6.2                
##  [87] rsvd_1.0.5                fansi_1.0.6              
##  [89] S4Arrays_1.4.0            viridisLite_0.4.2        
##  [91] dplyr_1.1.4               gtable_0.3.5             
##  [93] sass_0.4.9                digest_0.6.35            
##  [95] SparseArray_1.4.0         ggrepel_0.9.5            
##  [97] farver_2.1.1              memoise_2.0.1            
##  [99] htmltools_0.5.8.1         lifecycle_1.0.4          
## [101] httr_1.4.7                statmod_1.5.0            
## [103] mime_0.12                 bit64_4.0.5