Package: lisaClust 1.15.6

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_1.15.6.tar.gz
lisaClust_1.15.6.zip(r-4.5)lisaClust_1.15.6.zip(r-4.4)lisaClust_1.15.6.zip(r-4.3)
lisaClust_1.15.6.tgz(r-4.4-any)lisaClust_1.15.6.tgz(r-4.3-any)
lisaClust_1.15.6.tar.gz(r-4.5-noble)lisaClust_1.15.6.tar.gz(r-4.4-noble)
lisaClust_1.15.6.tgz(r-4.4-emscripten)lisaClust_1.15.6.tgz(r-4.3-emscripten)
lisaClust.pdf |lisaClust.html✨
lisaClust/json (API)

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

Peer review:

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

On BioConductor:lisaClust-1.15.6(bioc 3.21)lisaClust-1.14.4(bioc 3.20)

singlecellcellbasedassaysspatial

6.60 score 3 stars 44 scripts 280 downloads 8 exports 215 dependencies

Last updated 2 months agofrom:a5842b8284. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 19 2025
R-4.5-winNOTEJan 19 2025
R-4.5-linuxNOTEJan 19 2025
R-4.4-winNOTEJan 19 2025
R-4.4-macNOTEJan 19 2025
R-4.3-winNOTEJan 19 2025
R-4.3-macNOTEJan 19 2025

Exports:geom_hatchinghatchingPlotinhomLocalKlisalisaClustregionMapscale_regionscale_region_manual

Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encbdsmatrixbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDataclassClassifyRclassIntclicodetoolscolorspacecommonmarkconcavemancorrplotcowplotcoxmecpp11crayoncurlcytomapperdata.tableDBIdbplyrDelayedArraydeldirDerivdigestdoBydplyre1071EBImageevaluatefansifarverfastmapfftwtoolsfilelockfontawesomeformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggforceggh4xggnewscaleggplot2ggpubrggrepelggsciggsignifggthemesggupsetgluegoftestgridExtragtableHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelifecyclelme4lmerTestlocfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentmunsellnlmenloptrnnetnnlsnumDerivopensslpbkrtestpheatmappillarpkgconfigplogrplyrpngpolyclippolynompromisesproxypurrrquantregR6rangerrappdirsrasterrbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLiterstatixs2S4ArraysS4VectorssassscalesscamsfshinyshinydashboardsimpleSegSingleCellExperimentsnowsourcetoolsspSparseArraySparseMSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsspicyRstringistringrSummarizedExperimentsurvivalsvglitesvgPanZoomsyssystemfontstensorterratibbletidyrtidyselecttifftinytextweenrUCSC.utilsunitsutf8V8vctrsviporviridisviridisLitewithrwkxfunXMLxtableXVectoryaml

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

Nicolas Canete, Ellis Patrick, Alex Run Qin

Rendered fromlisaClust.Rmdusingknitr::rmarkdownon Jan 19 2025.

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