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) (2024-03-18 r86148)
## 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_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_1.13.1             
##  [3] reshape2_1.4.4              ggplot2_3.5.0              
##  [5] scviR_1.3.3                 SingleCellExperiment_1.25.0
##  [7] SummarizedExperiment_1.33.3 Biobase_2.63.0             
##  [9] GenomicRanges_1.55.4        GenomeInfoDb_1.39.9        
## [11] IRanges_2.37.1              S4Vectors_0.41.5           
## [13] BiocGenerics_0.49.1         MatrixGenerics_1.15.0      
## [15] matrixStats_1.2.0           shiny_1.8.0                
## [17] basilisk_1.15.5             reticulate_1.35.0          
## [19] BiocStyle_2.31.0           
## 
## 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_2.3.5            
##   [7] mgcv_1.9-1                dir.expiry_1.11.0        
##   [9] DelayedMatrixStats_1.25.1 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_0.43.1           
##  [19] ellipsis_0.3.2            labeling_0.4.3           
##  [21] utf8_1.2.4                promises_1.2.1           
##  [23] rmarkdown_2.26            ggbeeswarm_0.7.2         
##  [25] purrr_1.0.2               bit_4.0.5                
##  [27] xfun_0.42                 zlibbioc_1.49.3          
##  [29] cachem_1.0.8              beachmat_2.19.1          
##  [31] jsonlite_1.8.8            blob_1.2.4               
##  [33] highr_0.10                later_1.3.2              
##  [35] DelayedArray_0.29.9       BiocParallel_1.37.1      
##  [37] irlba_2.3.5.1             parallel_4.4.0           
##  [39] R6_2.5.1                  stringi_1.8.3            
##  [41] RColorBrewer_1.1-3        bslib_0.6.1              
##  [43] limma_3.59.6              jquerylib_0.1.4          
##  [45] Rcpp_1.0.12               bookdown_0.38            
##  [47] knitr_1.45                splines_4.4.0            
##  [49] httpuv_1.6.14             Matrix_1.6-5             
##  [51] tidyselect_1.2.1          abind_1.4-5              
##  [53] yaml_2.3.8                viridis_0.6.5            
##  [55] codetools_0.2-19          curl_5.2.1               
##  [57] plyr_1.8.9                lattice_0.22-6           
##  [59] tibble_3.2.1              withr_3.0.0              
##  [61] basilisk.utils_1.15.1     evaluate_0.23            
##  [63] BiocFileCache_2.11.1      pillar_1.9.0             
##  [65] BiocManager_1.30.22       filelock_1.0.3           
##  [67] generics_0.1.3            sparseMatrixStats_1.15.0 
##  [69] munsell_0.5.0             scales_1.3.0             
##  [71] xtable_1.8-4              glue_1.7.0               
##  [73] pheatmap_1.0.12           tools_4.4.0              
##  [75] BiocNeighbors_1.21.2      ScaledMatrix_1.11.1      
##  [77] cowplot_1.1.3             grid_4.4.0               
##  [79] colorspace_2.1-0          nlme_3.1-164             
##  [81] GenomeInfoDbData_1.2.11   beeswarm_0.4.0           
##  [83] BiocSingular_1.19.0       vipor_0.4.7              
##  [85] cli_3.6.2                 rsvd_1.0.5               
##  [87] fansi_1.0.6               S4Arrays_1.3.6           
##  [89] viridisLite_0.4.2         dplyr_1.1.4              
##  [91] gtable_0.3.4              sass_0.4.9               
##  [93] digest_0.6.35             SparseArray_1.3.4        
##  [95] ggrepel_0.9.5             farver_2.1.1             
##  [97] memoise_2.0.1             htmltools_0.5.7          
##  [99] lifecycle_1.0.4           httr_1.4.7               
## [101] statmod_1.5.0             mime_0.12                
## [103] bit64_4.0.5