Package: ProFAST 1.4
Wei Liu
ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction
Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations. More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.
Authors:
ProFAST_1.4.tar.gz
ProFAST_1.4.tar.gz(r-4.5-noble)ProFAST_1.4.tar.gz(r-4.4-noble)
ProFAST_1.4.tgz(r-4.4-emscripten)
ProFAST.pdf |ProFAST.html✨
ProFAST/json (API)
# Install 'ProFAST' in R: |
install.packages('ProFAST', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/feiyoung/profast/issues
- CosMx_subset - A Seurat object including spatial transcriptomics dataset from CosMx platform
- pbmc3k_subset - A Seurat object including scRNA-seq PBMC dataset
- top5_signatures - A data.frame object including top five signature genes in scRNA-seq PBMC dataset
Last updated 9 months agofrom:e1b450bc3a. Checks:OK: 1 WARNING: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 14 2024 |
R-4.5-linux-x86_64 | WARNING | Nov 14 2024 |
Exports:AddAdjAddParSettingFASTcoembed_plotcoembedding_umapdiagnostic.cor.eigsFASTFAST_runFAST_singleFAST_structurefind.signature.genesget_r2_mcfaddenget.top.signature.datIntegrateSRTDataiscmeb_runmodel_set_FASTNCFMNCFM_fastpdistanceRunHarmonyLouvainRuniSCMEBSelectHKgenestransferGeneNames
Dependencies:abindAnnotationDbiaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelBiocSingularbiomaRtBiostringsbitbit64bitopsblobbootbroombslibcachemCairocarcarDatacaToolscliclustercodetoolscolorspacecommonmarkCompQuadFormcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirDerivdigestdoBydotCall64dplyrdqrngDR.SCevaluatefansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomeformatRFormulafsfurrrfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggpubrggrastrggrepelggridgesggsciggsignifggthemesGiRaFglobalsgluegoftestgplotsgridExtragtablegtoolsharmonyherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelistenvlme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoisemgcvmicrobenchmarkmimeminiUIminqamodelrmunsellnlmenloptrnnetnumDerivopensslorg.Hs.eg.dborg.Mm.eg.dbparallellypatchworkpbapplypbkrtestpheatmappillarpkgconfigplogrplotlyplyrpngpolyclippolynomPRECASTprettyunitsprogressprogressrpromisespurrrquantregR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulateRhpcBLASctlrlangrmarkdownROCRrprojrootRSpectraRSQLiterstatixrsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermoresctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraySparseMspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunxml2xtableXVectoryamlzlibbioczoo
CoFAST: NSCLC CosMx data coembedding
Rendered fromCosMx.Rmd
usingknitr::rmarkdown
on Nov 14 2024.Last update: 2024-03-19
Started: 2024-03-19
CoFAST: PBMC scRNA-seq data coembedding
Rendered frompbmc3k.Rmd
usingknitr::rmarkdown
on Nov 14 2024.Last update: 2024-03-19
Started: 2024-03-19
FAST: simulation
Rendered fromFASTsimu.Rmd
usingknitr::rmarkdown
on Nov 14 2024.Last update: 2024-01-12
Started: 2024-01-12
FAST: single DLPFC section
Rendered fromFASTdlpfc.Rmd
usingknitr::rmarkdown
on Nov 14 2024.Last update: 2024-03-19
Started: 2024-03-19
FAST: two DLPFC sections
Rendered fromFASTdlpfc2.Rmd
usingknitr::rmarkdown
on Nov 14 2024.Last update: 2024-03-19
Started: 2024-01-12