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 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
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## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.22-bioc/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
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## [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_1.9.14 shiny_1.11.1
## [3] basilisk_1.21.5 reticulate_1.43.0
## [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_1.61.6 Seqinfo_0.99.3
## [13] IRanges_2.43.5 S4Vectors_0.47.4
## [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 crayon_1.5.3 fastmap_1.2.0
## [16] magick_2.9.0 dbplyr_2.5.1 XVector_0.49.1
## [19] labeling_0.4.3 promises_1.4.0 rmarkdown_2.30
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## [58] evaluate_1.0.5 BiocFileCache_2.99.6 pillar_1.11.1
## [61] BiocManager_1.30.26 filelock_1.0.3 scales_1.4.0
## [64] xtable_1.8-4 glue_1.8.0 pheatmap_1.0.13
## [67] tools_4.5.1 BiocNeighbors_2.3.1 ScaledMatrix_1.17.0
## [70] cowplot_1.2.0 grid_4.5.1 nlme_3.1-168
## [73] beeswarm_0.4.0 BiocSingular_1.25.0 vipor_0.4.7
## [76] cli_3.6.5 rsvd_1.0.5 rappdirs_0.3.3
## [79] S4Arrays_1.9.1 viridisLite_0.4.2 dplyr_1.1.4
## [82] gtable_0.3.6 sass_0.4.10 digest_0.6.37
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## [91] statmod_1.5.1 mime_0.13 bit64_4.6.0-1