Package: scider 1.5.0

Yunshun Chen

scider: Spatial cell-type inter-correlation by density in R

scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

Authors:Ning Liu [aut], Mengbo Li [aut], Yunshun Chen [aut, cre]

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scider.pdf |scider.html✨
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NEWS

# Install 'scider' in R:
install.packages('scider', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/chenlaboratory/scider/issues

Datasets:

    On BioConductor:scider-1.5.0(bioc 3.21)scider-1.4.0(bioc 3.20)

    spatialtranscriptomics

    4.90 score 2 stars 3 scripts 113 downloads 16 exports 134 dependencies

    Last updated 25 days agofrom:5152c7e40b. Checks:OK: 7. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKNov 19 2024
    R-4.5-winOKNov 19 2024
    R-4.5-linuxOKNov 19 2024
    R-4.4-winOKNov 19 2024
    R-4.4-macOKNov 19 2024
    R-4.3-winOKNov 19 2024
    R-4.3-macOKNov 19 2024

    Exports:allocateCellscorDensityfindROIgetContourgridDensitymergeROIplotCellCompoplotContourplotCorHeatmapplotDensCorplotDensityplotROIplotSpatialpostSelRegionselectRegionspe2PB

    Dependencies:abindaskpassbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbslibcachemclassclassIntclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdplyre1071evaluatefansifarverfastmapfilelockfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegoftestgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjanitorjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelubridatelwgeommagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpheatmappillarpkgconfigplogrplotlypolyclippromisesproxypurrrR6rappdirsRColorBrewerRcpprjsonrlangrmarkdownRSQLites2S4ArraysS4VectorssassscalessfshinySingleCellExperimentsnakecasesourcetoolsSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensortibbletidyrtidyselecttimechangetinytexUCSC.utilsunitsutf8vctrsviridisLitewithrwkxfunxtableXVectoryamlzlibbioc

    A quick start guide to the scider package

    Ning Liu, Mengbo Li, Yunshun Chen

    Rendered fromscider_userGuide.Rmdusingknitr::rmarkdownon Nov 19 2024.

    Last update: 2023-10-30
    Started: 2023-10-30