Package: hoodscanR 1.9.0

Ning Liu

hoodscanR: Spatial cellular neighbourhood scanning in R

hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.

Authors:Ning Liu [aut, cre], Jarryd Martin [aut]

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hoodscanR.pdf |hoodscanR.html✨
hoodscanR/json (API)
NEWS

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

Bug tracker:https://github.com/davislaboratory/hoodscanr/issues

Pkgdown/docs site:https://davislaboratory.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:hoodscanR-1.9.0(bioc 3.23)hoodscanR-1.8.0(bioc 3.22)

spatialtranscriptomicssinglecellclusteringcpp

5.60 score 12 stars 33 scripts 308 downloads 12 exports 100 dependencies

Last updated from:fbbd3998d7. Checks:1 NOTE, 12 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE185
linux-devel-arm64OK269
linux-devel-x86_64OK353
source / vignettesOK285
linux-release-arm64OK272
linux-release-x86_64OK356
macos-devel-arm64OK198
macos-devel-x86_64OK382
macos-release-arm64OK159
macos-release-x86_64OK378
windows-develOK243
windows-releaseOK233
wasm-releaseOK157

Exports:calcMetricsclustByHoodfindNearCellsmergeByGroupmergeHoodSpeperplexityPermuteplotColocalplotHoodMatplotProbDistplotTissuereadHoodDatascanHoods

Dependencies:abindaskpassbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbslibcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdbplyrDelayedArraydigestdoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachfsgenericsGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehighrhtmltoolshttr2IRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6RANNrappdirsRColorBrewerRcpprjsonrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesscicoSeqinfoshapeSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

A quick start guide to the hoodscanR package

Ning Liu, Melissa Davis

Rendered fromQuick_start.Rmdusingknitr::rmarkdownon Mar 23 2026.

Last update: 2023-09-25
Started: 2023-08-14

Readme and manuals

Help Manual

Help pageTopics
Calculate metrics for probability matrixcalcMetrics
Cluster the probability matrix with K-meansclustByHood clustByHood,matrix-method clustByHood,SpatialExperiment-method
Find the k-th nearest cells for each cellfindNearCells
Merge probability matrix based on annotationsmergeByGroup
Merge probability matrix into SpatialExperiment object.mergeHoodSpe
Compute p-value for perplexity via permutationperplexityPermute
Plot heatmap for neighbourhood analysisplotColocal plotColocal,matrix-method plotColocal,SpatialExperiment-method
Plot probability matrix as a heatmapplotHoodMat plotHoodMat,matrix-method plotHoodMat,SpatialExperiment-method
Plot probability distributionplotProbDist plotProbDist,matrix-method plotProbDist,SpatialExperiment-method
Plot cells based on cell position on tissue.plotTissue
Read cellular position and annotation data into a list object.readHoodData
Scan cellular neighbourhoods.scanHoods