Package: scviR 1.7.0

Vincent Carey

scviR: experimental inferface from R to scvi-tools

This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

Authors:Vincent Carey [aut, cre]

scviR_1.7.0.tar.gz
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scviR_1.7.0.tgz(r-4.4-any)scviR_1.7.0.tgz(r-4.3-any)
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scviR.pdf |scviR.html✨
scviR/json (API)

# Install 'scviR' in R:

install.packages('scviR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vjcitn/scvir/issues

Datasets:

clusters.adt - ADT-based cluster labels for 7472 cells in OSCA chapter 12 analysis
clusters.rna - MRNA-based cluster labels for 7472 cells in OSCA chapter 12 analysis

On BioConductor:scviR-1.7.0(bioc 3.21)scviR-1.6.0(bioc 3.20)

infrastructure singlecell dataimport bioconductor cite-seq scverse

5.69 score 6 stars 11 scripts 124 downloads 20 exports 140 dependencies

Last updated 22 days agofrom:97c87b8c46. Checks:OK: 1 NOTE: 3 ERROR: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	ERROR	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	ERROR	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	ERROR	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:adtProfiles anndataR cacheCiteseq5k10kPbmcs cacheCiteseq5k10kTutvae exploreSubcl getCh12AllSce getCh12Sce getCiteseq5k10kPbmcs getCiteseqTutvae getPro5k10kAdata getSubclLM getSubclusteringFeatures getTotalVI5k10kAdata getTotalVINormalized5k10k MuDataR pyHelp2 scanpyHelper scanpyR scviHelper scviR

Dependencies:abind askpass assorthead base64enc basilisk basilisk.utils beachmat beeswarm BH Biobase BiocFileCache BiocGenerics BiocNeighbors BiocParallel BiocSingular bit bit64 blob bslib cachem Cairo cli codetools colorspace commonmark cpp11 crayon curl DBI dbplyr DelayedArray digest dir.expiry dplyr dqrng fansi farver fastmap filelock FNN fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggplot2 ggrastr ggrepel glue gridExtra gtable here htmltools httpuv httr IRanges irlba isoband jquerylib jsonlite labeling lambda.r later lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pheatmap pillar pkgconfig plogr png promises purrr R6 ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppEigen RcppML RcppProgress RcppTOML reticulate rlang rprojroot RSpectra RSQLite rsvd Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scater scuttle shiny SingleCellExperiment sitmo snow sourcetools SparseArray statmod stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidyr tidyselect UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr xtable XVector zlibbioc

Comparing totalVI and OSCA book CITE-seq analyses

OSCA book authors and Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromcompch12.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-01-27
Started: 2023-02-17

scvi-tools CITE-seq tutorial in R, using serialized tutorial components

Follows scvi-tools doc, Gayoso, Steier et al. DOI 10.1038/s41592-020-01050-x

Rendered fromciteseq_tut.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-03-10
Started: 2023-02-05

scviR: an R package interfacing Bioconductor and scvi-tools

Vince Carey stvjc at channing.harvard.edu

Rendered fromscviR.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-03-10
Started: 2023-01-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
produce a heatmap from a specialized CITE-seq SingleCellExperiment	adtProfiles
basic interface to anndata	anndataR
python declarations	bsklenv
grab scvi-tools-processed PBMC CITE-seq data in anndata format (gzipped) from Open Storage Network	cacheCiteseq5k10kPbmcs
grab scvi-tools VAE instance built on the PBMC datasets following the tutorial	cacheCiteseq5k10kTutvae
ADT-based cluster labels for 7472 cells in OSCA chapter 12 analysis	clusters.adt
mRNA-based cluster labels for 7472 cells in OSCA chapter 12 analysis	clusters.rna
app to explore diversity in RNA-subclusters within ADT clusters	exploreSubcl
get list of cluster-specific SCE for 10k PBMC annotated as in OSCA book chapter 12	getCh12AllSce
get SCE for 10k PBMC annotated as in OSCA book chapter 12	getCh12Sce
helper to get the processed anndata for CITE-seq PBMCs from scvi-tools tutorial	getCiteseq5k10kPbmcs
helper to get the tutorial VAE for PBMCs from scvi-tools tutorial	getCiteseqTutvae
get an anndata reference to 5k10k protein after totalVI from tutorial	getPro5k10kAdata
get lmFit for heterogeneity across subclusters	getSubclLM
get lmFit F-stat based collection of n genes most varying in mean across subclusters	getSubclusteringFeatures
get anndata reference to full totalVI processing of 5k10k data	getTotalVI5k10kAdata
get matrices of normalized quantifications from full totalVI 5k10k from tutorial	getTotalVINormalized5k10k
basic interface to MuData	MuDataR
helper to get text from python help utility - may need handling through basilisk	pyHelp2
shiny app that helps access documentation on python-accessible components	scanpyHelper
basic interface	scanpyR
shiny app that helps access documentation on python-accessible components	scviHelper
basic interface	scviR