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'))

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

Pkgdown site:https://chenlaboratory.github.io

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

spatialtranscriptomics

5.08 score 3 stars 3 scripts 147 downloads 16 exports 133 dependencies

Last updated 4 months agofrom:5152c7e40b. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winOKFeb 17 2025
R-4.5-macOKFeb 17 2025
R-4.5-linuxOKFeb 17 2025
R-4.4-winOKFeb 17 2025
R-4.4-macOKFeb 17 2025
R-4.3-winOKFeb 17 2025
R-4.3-macOKFeb 17 2025

Exports:allocateCellscorDensityfindROIgetContourgridDensitymergeROIplotCellCompoplotContourplotCorHeatmapplotDensCorplotDensityplotROIplotSpatialpostSelRegionselectRegionspe2PB

Dependencies:abindaskpassbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbslibcachemclassclassIntclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdplyre1071evaluatefansifarverfastmapfilelockfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegoftestgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjanitorjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelubridatelwgeommagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpheatmappillarpkgconfigplogrplotlypolyclippromisesproxypurrrR6rappdirsRColorBrewerRcpprjsonrlangrmarkdownRSQLites2S4ArraysS4VectorssassscalessfshinySingleCellExperimentsnakecasesourcetoolsSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensortibbletidyrtidyselecttimechangetinytexUCSC.utilsunitsutf8vctrsviridisLitewithrwkxfunxtableXVectoryaml

A quick start guide to the scider package

Ning Liu, Mengbo Li, Yunshun Chen

Rendered fromscider_userGuide.Rmdusingknitr::rmarkdownon Feb 17 2025.

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