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 Under development (unstable) (2026-02-04 r89376)
## 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-3.23-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_1.11.1 shiny_1.12.1
## [3] basilisk_1.23.0 reticulate_1.45.0
## [5] scater_1.39.2 ggplot2_4.0.2
## [7] scuttle_1.21.0 SingleCellExperiment_1.33.0
## [9] SummarizedExperiment_1.41.1 Biobase_2.71.0
## [11] GenomicRanges_1.63.1 Seqinfo_1.1.0
## [13] IRanges_2.45.0 S4Vectors_0.49.0
## [15] BiocGenerics_0.57.0 generics_0.1.4
## [17] MatrixGenerics_1.23.0 matrixStats_1.5.0
## [19] BiocStyle_2.39.0
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## loaded via a namespace (and not attached):
## [1] DBI_1.2.3 gridExtra_2.3 httr2_1.2.2
## [4] rlang_1.1.7 magrittr_2.0.4 otel_0.2.0
## [7] compiler_4.6.0 RSQLite_2.4.6 mgcv_1.9-4
## [10] dir.expiry_1.19.0 png_0.1-8 vctrs_0.7.1
## [13] pkgconfig_2.0.3 fastmap_1.2.0 dbplyr_2.5.2
## [16] XVector_0.51.0 labeling_0.4.3 promises_1.5.0
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## [52] tibble_3.3.1 withr_3.0.2 S7_0.2.1
## [55] evaluate_1.0.5 BiocFileCache_3.1.0 pillar_1.11.1
## [58] BiocManager_1.30.27 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_4.6.0 BiocNeighbors_2.5.4
## [67] ScaledMatrix_1.19.0 cowplot_1.2.0 grid_4.6.0
## [70] nlme_3.1-168 beeswarm_0.4.0 BiocSingular_1.27.1
## [73] vipor_0.4.7 cli_3.6.5 rsvd_1.0.5
## [76] rappdirs_0.3.4 S4Arrays_1.11.1 viridisLite_0.4.3
## [79] dplyr_1.2.0 gtable_0.3.6 sass_0.4.10
## [82] digest_0.6.39 SparseArray_1.11.10 ggrepel_0.9.6
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