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:
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
getCh12AllSce() (74 MB will be retrieved and cached)getCh12Sce() (58 MB will be retrieved and cached)getTotalVINormalized5k10k() (191 MB will be retrieved and cached)## R version 4.5.0 Patched (2025-05-01 r88189)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /media/volume/biocgpu/biocbuild/bbs-3.22-bioc-gpu/R/lib/libRblas.so
## LAPACK: /media/volume/biocgpu/biocbuild/bbs-3.22-bioc-gpu/R/lib/libRlapack.so; LAPACK version 3.12.1
##
## 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_1.10.0
## [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 dbplyr_2.5.0
## [16] XVector_0.49.0 labeling_0.4.3 promises_1.3.2
## [19] rmarkdown_2.29 UCSC.utils_1.5.0 ggbeeswarm_0.7.2
## [22] tinytex_0.57 purrr_1.0.4 bit_4.6.0
## [25] xfun_0.52 cachem_1.1.0 beachmat_2.25.0
## [28] jsonlite_2.0.0 blob_1.2.4 later_1.4.2
## [31] DelayedArray_0.35.1 BiocParallel_1.43.0 irlba_2.3.5.1
## [34] parallel_4.5.0 R6_2.6.1 bslib_0.9.0
## [37] RColorBrewer_1.1-3 limma_3.65.0 jquerylib_0.1.4
## [40] Rcpp_1.0.14 bookdown_0.43 knitr_1.50
## [43] splines_4.5.0 httpuv_1.6.16 Matrix_1.7-3
## [46] tidyselect_1.2.1 abind_1.4-8 yaml_2.3.10
## [49] viridis_0.6.5 codetools_0.2-20 curl_6.2.2
## [52] lattice_0.22-7 tibble_3.2.1 basilisk.utils_1.21.0
## [55] withr_3.0.2 evaluate_1.0.3 BiocFileCache_2.99.0
## [58] pillar_1.10.2 BiocManager_1.30.25 filelock_1.0.3
## [61] scales_1.4.0 xtable_1.8-4 glue_1.8.0
## [64] pheatmap_1.0.12 tools_4.5.0 BiocNeighbors_2.3.0
## [67] ScaledMatrix_1.17.0 grid_4.5.0 nlme_3.1-168
## [70] beeswarm_0.4.0 BiocSingular_1.25.0 vipor_0.4.7
## [73] cli_3.6.5 rsvd_1.0.5 rappdirs_0.3.3
## [76] S4Arrays_1.9.0 viridisLite_0.4.2 dplyr_1.1.4
## [79] gtable_0.3.6 sass_0.4.10 digest_0.6.37
## [82] SparseArray_1.9.0 ggrepel_0.9.6 farver_2.1.2
## [85] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4
## [88] httr_1.4.7 statmod_1.5.0 mime_0.13
## [91] bit64_4.6.0-1