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 Under development (unstable) (2024-01-16 r85808)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.3 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_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] scater_1.31.2               scuttle_1.13.0             
##  [3] reshape2_1.4.4              ggplot2_3.4.4              
##  [5] scviR_1.3.1                 SingleCellExperiment_1.25.0
##  [7] SummarizedExperiment_1.33.3 Biobase_2.63.0             
##  [9] GenomicRanges_1.55.2        GenomeInfoDb_1.39.5        
## [11] IRanges_2.37.1              S4Vectors_0.41.3           
## [13] BiocGenerics_0.49.1         MatrixGenerics_1.15.0      
## [15] matrixStats_1.2.0           shiny_1.8.0                
## [17] basilisk_1.15.3             reticulate_1.34.0          
## [19] BiocStyle_2.31.0           
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.1                 bitops_1.0-7             
##   [3] gridExtra_2.3             rlang_1.1.3              
##   [5] magrittr_2.0.3            compiler_4.4.0           
##   [7] RSQLite_2.3.5             mgcv_1.9-1               
##   [9] dir.expiry_1.11.0         DelayedMatrixStats_1.25.1
##  [11] png_0.1-8                 vctrs_0.6.5              
##  [13] stringr_1.5.1             pkgconfig_2.0.3          
##  [15] crayon_1.5.2              fastmap_1.1.1            
##  [17] magick_2.8.2              dbplyr_2.4.0             
##  [19] XVector_0.43.1            ellipsis_0.3.2           
##  [21] labeling_0.4.3            utf8_1.2.4               
##  [23] promises_1.2.1            rmarkdown_2.25           
##  [25] ggbeeswarm_0.7.2          purrr_1.0.2              
##  [27] bit_4.0.5                 xfun_0.41                
##  [29] zlibbioc_1.49.0           cachem_1.0.8             
##  [31] beachmat_2.19.1           jsonlite_1.8.8           
##  [33] blob_1.2.4                highr_0.10               
##  [35] later_1.3.2               DelayedArray_0.29.0      
##  [37] BiocParallel_1.37.0       irlba_2.3.5.1            
##  [39] parallel_4.4.0            R6_2.5.1                 
##  [41] stringi_1.8.3             RColorBrewer_1.1-3       
##  [43] bslib_0.6.1               limma_3.59.1             
##  [45] jquerylib_0.1.4           Rcpp_1.0.12              
##  [47] bookdown_0.37             knitr_1.45               
##  [49] splines_4.4.0             httpuv_1.6.14            
##  [51] Matrix_1.6-5              tidyselect_1.2.0         
##  [53] abind_1.4-5               yaml_2.3.8               
##  [55] viridis_0.6.4             codetools_0.2-19         
##  [57] curl_5.2.0                plyr_1.8.9               
##  [59] lattice_0.22-5            tibble_3.2.1             
##  [61] withr_3.0.0               basilisk.utils_1.15.1    
##  [63] evaluate_0.23             BiocFileCache_2.11.1     
##  [65] pillar_1.9.0              BiocManager_1.30.22      
##  [67] filelock_1.0.3            generics_0.1.3           
##  [69] RCurl_1.98-1.14           sparseMatrixStats_1.15.0 
##  [71] munsell_0.5.0             scales_1.3.0             
##  [73] xtable_1.8-4              glue_1.7.0               
##  [75] pheatmap_1.0.12           tools_4.4.0              
##  [77] BiocNeighbors_1.21.2      ScaledMatrix_1.11.0      
##  [79] cowplot_1.1.3             grid_4.4.0               
##  [81] colorspace_2.1-0          nlme_3.1-164             
##  [83] GenomeInfoDbData_1.2.11   beeswarm_0.4.0           
##  [85] BiocSingular_1.19.0       vipor_0.4.7              
##  [87] cli_3.6.2                 rsvd_1.0.5               
##  [89] fansi_1.0.6               S4Arrays_1.3.2           
##  [91] viridisLite_0.4.2         dplyr_1.1.4              
##  [93] gtable_0.3.4              sass_0.4.8               
##  [95] digest_0.6.34             SparseArray_1.3.3        
##  [97] ggrepel_0.9.5             farver_2.1.1             
##  [99] memoise_2.0.1             htmltools_0.5.7          
## [101] lifecycle_1.0.4           httr_1.4.7               
## [103] statmod_1.5.0             mime_0.12                
## [105] bit64_4.0.5