cran
. See also theR-universe documentation.Package: PRECAST 1.6.5
Wei Liu
PRECAST: Embedding and Clustering with Alignment for Spatial Datasets
An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.
Authors:
PRECAST_1.6.5.tar.gz
PRECAST_1.6.5.tar.gz(r-4.5-noble)PRECAST_1.6.5.tar.gz(r-4.4-noble)
PRECAST_1.6.5.tgz(r-4.4-emscripten)
PRECAST.pdf |PRECAST.html✨
PRECAST/json (API)
# Install 'PRECAST' in R: |
install.packages('PRECAST', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/feiyoung/precast/issues
- Human_HK_genes - Human housekeeping genes database
- Mouse_HK_genes - Mouse housekeeping genes database
- PRECASTObj - A simple PRECASTObj for example
Last updated 9 months agofrom:ca0b851412. Checks:OK: 1 WARNING: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 15 2024 |
R-4.5-linux-x86_64 | WARNING | Nov 15 2024 |
Exports:Add_embedAddAdjListAddParSettingAddTSNEAddUMAPboxPlotchooseColorscoordinate_rotateCreatePRECASTObjectdimPlotdoHeatmapdrawFigsfeaturePlotfirstupgetAdj_fixedNumbergetAdj_regICM.EMICM.EM_structureIntegrateSpaDatamodel_setplot_RGBplot_scatterPRECASTSelectModelSelectModel.PRECASTObjSelectModel.SeqK_PRECAST_ObjectSpaPlotvolinPlot
Dependencies:abindaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsbootbroombslibcachemCairocarcarDatacaToolscliclustercodetoolscolorspacecommonmarkCompQuadFormcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirDerivdigestdoBydotCall64dplyrdqrngDR.SCevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggpubrggrastrggrepelggridgesggsciggsignifggthemesGiRaFglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelistenvlme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoisemgcvmicrobenchmarkmimeminiUIminqamodelrmunsellnlmenloptrnnetnumDerivopensslparallellypatchworkpbapplypbkrtestpheatmappillarpkgconfigplotlyplyrpngpolyclippolynomprogressrpromisespurrrquantregR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarstatixrsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermoresctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraySparseMspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunxtableXVectoryamlzlibbioczoo
PRECAST: installation
Rendered fromPRECAST.Rmd
usingknitr::rmarkdown
on Nov 15 2024.Last update: 2022-06-22
Started: 2022-06-22
PRECAST: DLPFC Single Sample Analysis
Rendered fromPRECAST.DLPFC.Rmd
usingknitr::rmarkdown
on Nov 15 2024.Last update: 2023-04-18
Started: 2022-10-18
PRECAST: Four DLPFC Sample Analysis
Rendered fromPRECAST.DLPFC4.Rmd
usingknitr::rmarkdown
on Nov 15 2024.Last update: 2024-01-26
Started: 2024-01-26
PRECAST: Human Breast Cancer Data Analysis
Rendered fromPRECAST.BreastCancer.Rmd
usingknitr::rmarkdown
on Nov 15 2024.Last update: 2024-01-26
Started: 2022-10-18
PRECAST: simulation
Rendered fromPRECAST.Simu.Rmd
usingknitr::rmarkdown
on Nov 15 2024.Last update: 2023-08-09
Started: 2022-06-22