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:
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')) |
Bug tracker:https://github.com/ellispatrick/lisaclust/issues
On BioConductor:lisaClust-1.15.0(bioc 3.21)lisaClust-1.14.4(bioc 3.20)
singlecellcellbasedassaysspatial
Last updated 1 months agofrom:a5842b8284. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win | NOTE | Nov 20 2024 |
| R-4.5-linux | NOTE | Nov 20 2024 |
| R-4.4-win | NOTE | Nov 20 2024 |
| R-4.4-mac | NOTE | Nov 20 2024 |
| R-4.3-win | NOTE | Nov 20 2024 |
| R-4.3-mac | NOTE | Nov 20 2024 |
Exports:geom_hatchinghatchingPlotinhomLocalKlisalisaClustregionMapscale_regionscale_region_manual
Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encbdsmatrixbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDataclassClassifyRclassIntclicodetoolscolorspacecommonmarkconcavemancorrplotcowplotcoxmecpp11crayoncurlcytomapperdata.tableDBIdbplyrDelayedArraydeldirDerivdigestdoBydplyre1071EBImageevaluatefansifarverfastmapfftwtoolsfilelockfontawesomeformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggforceggh4xggnewscaleggplot2ggpubrggrepelggsciggsignifggthemesggupsetgluegoftestgridExtragtableHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelifecyclelme4lmerTestlocfitmagickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentmunsellnlmenloptrnnetnnlsnumDerivopensslpbkrtestpheatmappillarpkgconfigplogrplyrpngpolyclippolynompromisesproxypurrrquantregR6rangerrappdirsrasterRColorBrewerRcppRcppEigenRCurlreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLiterstatixs2S4ArraysS4VectorssassscalesscamsfshinyshinydashboardsimpleSegSingleCellExperimentsnowsourcetoolsspSparseArraySparseMSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsspicyRstringistringrSummarizedExperimentsurvivalsvglitesvgPanZoomsyssystemfontstensorterratibbletidyrtidyselecttifftinytextweenrUCSC.utilsunitsutf8V8vctrsviporviridisviridisLitewithrwkxfunXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| hatchingPlot | geom_hatching hatchingPlot |
| Calculate the inhomogenous local K function. | inhomLocalK |
| Generate local indicators of spatial association | lisa |
| Use k-means clustering to cluster local indicators of spatial association. For other clustering use lisa. | lisaClust |
| Plot heatmap of cell type enrichment for lisaClust regions | regionMap |
| Scale constructor for regions | scale_region scale_region_manual |
