Package: scider 1.11.0

Yunshun Chen

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

scider is an 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 several downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

Authors:Mengbo Li, Ning Liu, Quoc Hoang Nguyen, Yunshun Chen

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manual.pdf |manual.html✨
card.svg |card.png
scider/json (API)
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/docs site:https://chenlaboratory.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:scider-1.11.0(bioc 3.24)scider-1.10.0(bioc 3.23)

spatialtranscriptomicscppopenjdk

6.30 score 11 stars 13 scripts 309 downloads 43 exports 182 dependencies

Last updated from:7dcb837f32. Checks:1 WARNING, 7 NOTE, 1 OK, 5 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING231
linux-devel-arm64NOTE420
linux-devel-x86_64NOTE501
source / vignettesOK362
linux-release-arm64NOTE408
linux-release-x86_64NOTE492
macos-release-arm64FAIL79
macos-release-x86_64FAIL198
macos-oldrel-arm64FAIL90
macos-oldrel-x86_64FAIL212
windows-develNOTE831
windows-releaseNOTE761
windows-oldrelNOTE808
wasm-releaseFAIL207

Exports:allocateCellscorDensityfindNbrsGridfindNbrsSNNfindNbrsSpatialfindROIgetClustersgetContourgetHVGgetNicheglobalMorangridDensitygridSPElocalMoranmergeROInormalizeAssayplotCellCompoplotContourplotCorHeatmapplotDensCorplotDensityplotDotsplotDRplotGridplotImageplotLISAplotLISAscatterplotPCAplotROIplotSpatialplotUMAPplotViolinpostSelRegionreadProsegreadVisiumreadVisiumHDreadXeniumrealignVisiumrealignVisiumHDrunPCArunUMAPselectRegionspe2PB

Dependencies:abindarrowaskpassassertthatassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocNeighborsBiocParallelbitbit64bitopsblobbslibcachemclassclassIntclicodetoolscommonmarkcpp11crosstalkcurldata.tableDBIdbplyrdbscanDelayedArrayDelayedMatrixStatsdeldirdigestdir.expirydplyrdqrngDropletUtilse1071EBImageedgeRevaluatefarverfastmapfastmatrixfftwtoolsfilelockFNNfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegoftestgtableh5mreadHDF5ArrayhexbinhexDensityhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesirlbaisobandjanitorjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitlubridatelwgeommagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslotelpheatmappillarpkgconfigplotlypngpolyclippromisesproxypurrrR.methodsS3R.ooR.utilsR6rappdirsRBioFormatsRColorBrewerRcppRcppAnnoyRcppEigenRcppProgressRCurlrhdf5rhdf5filtersRhdf5librJavarjsonrlangrmarkdownRSpectraRSQLites2S4ArraysS4VectorsS7sassscalesscuttleSeqinfosfshinySingleCellExperimentsitmosnakecasesnowsourcetoolsSparseArraysparseMatrixStatsSpatialExperimentSpatialPackspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsystensortibbletidyrtidyselecttifftimechangetinytexunitsutf8uwotvctrsviridisLitewithrwkxfunxtableXVectoryaml

A quick start guide to the scider package

Mengbo Li, Ning Liu, Quoc Hoang Nguyen and Yunshun Chen

Rendered fromscider_userGuide.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-10-03
Started: 2023-10-30

Readme and manuals

Help Manual

Help pageTopics
Subset for grid level analysis[,SpatialExperiment,ANY,ANY,ANY-method
Annotate all cells with contour level of cell type-specific density.allocateCells
Check which cells are in which regionscellsInRegion
Perform kernel density estimation on SpatialExperimentcomputeDensity
Perform kernel density estimation on SpatialExperimentcomputeDensityHex
Draw a contour region on some density levelcontour2sf
Hash two 15-bytes signed integers into one 32-bytes integer.coord_hash
Test for density correlation between two cell types.corDensity
Construct a neighbour list from grid coordinates.findNbrsGrid
Construct a SNN neighbour list from assay.findNbrsSNN
Construct a distance-based neighbour list from cell coordinates.findNbrsSpatial
Find ROIs based on cell type-specific densities via graph-based method.findROI
Cluster cells in spe using graph methods.getClusters
Get contour from densitygetContour
Calculate areas between every two density levelsgetContourRegions
Get top highly variable genes.getHVG
Build a niche assay based on the profile of neighbouring cellsgetNiche
Calculate global Moran for 1 to 2 variables.globalMoran
Convert x,y nodes to data.frame of polygonsgrid2df
Convert x,y nodes to sf polygonsgrid2sf
Perform kernel density estimation on SpatialExperiment for cell types of interestgridDensity
Summarize a SpatialExperiment object at grid-levelgridSPE
Calculate local Moran for 1 to 2 variables.localMoran
Manually merge ROIsmergeROI
Perform log normalization for countsnormalizeAssay
Plot cell type composition in each density level of cell of interest.plotCellCompo
Plot contour lines.plotContour
Visualising an sf object (for internal use only at the moment)plotContourRegion
Plot model statistics using heatmap.plotCorHeatmap
Plot density correlation between two cell typesplotDensCor
Plot grid-based density.plotDensity
Dot plot of gene expression by groupsplotDots
Plot reduced dimensions.plotDR plotPCA plotUMAP
Plot grid from metadata.plotGrid
Plot background image of speplotImage
Plotting LISA (e.g. moran)plotLISA
Scatterplot for local moran's IplotLISAscatter
Plot ROIs on spatial.plotROI
Plot cells based on spatial coordinates.plotSpatial
Violin plot using genes or cell dataplotViolin
Merge sel_region from the selectRegion function to SpatialExperiment.postSelRegion
Read Proseg V2 output into spereadProseg
Read Visium output into spereadVisium
Read VisiumHD output into spereadVisiumHD
Read Xenium output into spereadXenium
Scale and straighten out Visium coordinatesrealignVisium
Scale and straighten out VisiumHD coordinatesrealignVisiumHD
Fast PCA using irlba.runPCA
UMAP using uwot. Parameters are set to be similar to Seurat'srunUMAP
Select region of interest from plotselectRegion
Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList objectspe2PB
Update the x,y limits of a plotupdate_bound