Package: lisaClust 1.20.0

Ellis Patrick

lisaClust: lisaClust: Clustering of Local Indicators of Spatial Association

lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

Authors:Ellis Patrick [aut, cre], Nicolas Canete [aut], Nicholas Robertson [ctb], Alex Qin [ctb], Shreya [email protected] Rao [ctb]

lisaClust_1.20.0.tar.gz
lisaClust_1.20.0.zip(r-4.7)lisaClust_1.20.0.zip(r-4.6)lisaClust_1.20.0.zip(r-4.5)
lisaClust_1.20.0.tgz(r-4.6-any)lisaClust_1.20.0.tgz(r-4.5-any)
lisaClust_1.20.0.tar.gz(r-4.7-any)lisaClust_1.20.0.tar.gz(r-4.6-any)
lisaClust_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
lisaClust/json (API)

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

Bug tracker:https://github.com/ellispatrick/lisaclust/issues

On BioConductor:lisaClust-1.21.0(bioc 3.24)lisaClust-1.20.0(bioc 3.23)

singlecellcellbasedassaysspatial

6.13 score 4 stars 48 scripts 448 downloads 8 exports 233 dependencies

Last updated from:820c0e4e8c (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING260
linux-devel-x86_64NOTE476
source / vignettesOK510
linux-release-x86_64NOTE489
macos-release-arm64NOTE237
macos-oldrel-arm64NOTE209
windows-develNOTE391
windows-releaseNOTE394
windows-oldrelNOTE422
wasm-releaseOK248

Exports:geom_hatchinghatchingPlotinhomLocalKlisalisaClustregionMapscale_regionscale_region_manual

Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encbdsmatrixbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacirclizeclassClassifyRclassIntclicodetoolscolorspacecommonmarkconcavemancorrplotcowplotcoxmecpp11crayoncurlcytomapperdata.tableDBIdbplyrdcanrDelayedArraydeldirDerivdigestdir.expirydoBydoRNGdplyre1071EBImageevaluatefarverfastmapfftwtoolsfilelockfontawesomeforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenefiltergenericsGenomicRangesggbeeswarmggforceggh4xggnewscaleggplot2ggpubrggrepelggsciggsignifggthemesggupsetGlobalOptionsgluegoftestgridExtragtableh5mreadHDF5Arrayhighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelifecyclelme4lmerTestlmtestlocfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentnlmenloptrnnetnnlsnumDerivopensslotelpbkrtestpheatmappillarpkgconfigplyrpngpolyclippolynompromisesproxypurrrquantregR6rangerrappdirsrasterrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrngtoolsRSQLiterstatixs2S4ArraysS4VectorsS7sassscalesscamSeqinfosfshapeshinyshinydashboardsimpleSegSingleCellExperimentsnowsourcetoolsspSparseArraySparseMSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsspicyRstringistringrSummarizedExperimentsurvivalsvglitesvgPanZoomsyssystemfontstensorterratextshapingtibbletidyrtidyselecttifftimeDatetinytextweenrunitsurcautf8V8vctrsviporviridisviridisLitewithrwkxfunXMLxtableXVectoryamlzoo

Introduction to Clustering of Local Indicators of Spatial Assocation (LISA) curves

Nicolas Canete, Ellis Patrick, Alex Run Qin

Rendered fromlisaClust.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-10-08
Started: 2021-03-15