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 4.5.1 Patched (2025-08-23 r88803)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
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## Matrix products: default
## BLAS: /media/volume/biocgpu2/biocbuild/bbs-3.22-bioc-gpu/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
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## 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
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## time zone: America/New_York
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
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## other attached packages:
## [1] scviR_1.10.0 shiny_1.11.1
## [3] basilisk_1.21.5 reticulate_1.44.0
## [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_1.61.8 Seqinfo_0.99.4
## [13] IRanges_2.43.8 S4Vectors_0.47.6
## [15] BiocGenerics_0.55.4 generics_0.1.4
## [17] MatrixGenerics_1.21.0 matrixStats_1.5.0
## [19] BiocStyle_2.37.1
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## 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 otel_0.2.0
## [7] compiler_4.5.1 RSQLite_2.4.3 mgcv_1.9-3
## [10] dir.expiry_1.17.0 png_0.1-8 vctrs_0.6.5
## [13] pkgconfig_2.0.3 fastmap_1.2.0 dbplyr_2.5.1
## [16] XVector_0.49.3 labeling_0.4.3 promises_1.4.0
## [19] rmarkdown_2.30 ggbeeswarm_0.7.2 tinytex_0.57
## [22] purrr_1.1.0 bit_4.6.0 xfun_0.53
## [25] cachem_1.1.0 beachmat_2.25.5 jsonlite_2.0.0
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## [31] BiocParallel_1.43.4 irlba_2.3.5.1 parallel_4.5.1
## [34] R6_2.6.1 bslib_0.9.0 RColorBrewer_1.1-3
## [37] limma_3.65.7 jquerylib_0.1.4 Rcpp_1.1.0
## [40] bookdown_0.45 knitr_1.50 splines_4.5.1
## [43] httpuv_1.6.16 Matrix_1.7-4 tidyselect_1.2.1
## [46] abind_1.4-8 yaml_2.3.10 viridis_0.6.5
## [49] codetools_0.2-20 curl_7.0.0 lattice_0.22-7
## [52] tibble_3.3.0 withr_3.0.2 S7_0.2.0
## [55] evaluate_1.0.5 BiocFileCache_2.99.6 pillar_1.11.1
## [58] BiocManager_1.30.26 filelock_1.0.3 rprojroot_2.1.1
## [61] scales_1.4.0 xtable_1.8-4 glue_1.8.0
## [64] pheatmap_1.0.13 tools_4.5.1 BiocNeighbors_2.3.1
## [67] ScaledMatrix_1.17.0 cowplot_1.2.0 grid_4.5.1
## [70] nlme_3.1-168 beeswarm_0.4.0 BiocSingular_1.25.1
## [73] vipor_0.4.7 cli_3.6.5 rsvd_1.0.5
## [76] rappdirs_0.3.3 S4Arrays_1.9.2 viridisLite_0.4.2
## [79] dplyr_1.1.4 gtable_0.3.6 sass_0.4.10
## [82] digest_0.6.37 SparseArray_1.9.1 ggrepel_0.9.6
## [85] farver_2.1.2 memoise_2.0.1 htmltools_0.5.8.1
## [88] lifecycle_1.0.4 here_1.0.2 statmod_1.5.1
## [91] mime_0.13 bit64_4.6.0-1