Package: scviR 1.5.0
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:
scviR_1.5.0.tar.gz
scviR_1.5.0.zip(r-4.5)scviR_1.5.0.zip(r-4.4)scviR_1.5.0.zip(r-4.3)
scviR_1.5.0.tgz(r-4.4-any)scviR_1.5.0.tgz(r-4.3-any)
scviR_1.5.0.tar.gz(r-4.5-noble)scviR_1.5.0.tar.gz(r-4.4-noble)
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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
- 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-1.5.0(bioc 3.20)scviR-1.4.0(bioc 3.19)
Last updated 2 months agofrom:ff7fb3640f
Exports:adtProfilesanndataRcacheCiteseq5k10kPbmcscacheCiteseq5k10kTutvaeexploreSubclgetCh12AllScegetCh12ScegetCiteseq5k10kPbmcsgetCiteseqTutvaegetPro5k10kAdatagetSubclLMgetSubclusteringFeaturesgetTotalVI5k10kAdatagetTotalVINormalized5k10kMuDataRpyHelp2scanpyHelperscanpyRscviHelperscviR
Dependencies:abindaskpassbase64encbasiliskbasilisk.utilsbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiocSingularbitbit64blobbslibcachemCairoclicodetoolscolorspacecommonmarkcpp11crayoncurlDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydplyrdqrngfansifarverfastmapfilelockFNNfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtableherehtmltoolshttpuvhttrIRangesirlbaisobandjquerylibjsonlitelabelinglambda.rlaterlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpheatmappillarpkgconfigplogrpngpromisespurrrR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreticulaterlangrprojrootRSpectraRSQLitersvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscuttleshinySingleCellExperimentsitmosnowsourcetoolsSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxtableXVectorzlibbioc
Comparing totalVI and OSCA book CITE-seq analyses
Rendered fromcompch12.Rmd
usingknitr::rmarkdown
on Jun 11 2024.Last update: 2024-01-27
Started: 2023-02-17
scvi-tools CITE-seq tutorial in R, using serialized tutorial components
Rendered fromciteseq_tut.Rmd
usingknitr::rmarkdown
on Jun 11 2024.Last update: 2023-03-10
Started: 2023-02-05
scviR: an R package interfacing Bioconductor and scvi-tools
Rendered fromscviR.Rmd
usingknitr::rmarkdown
on Jun 11 2024.Last update: 2023-03-10
Started: 2023-01-26