Introduction | Installation | Tissue domains in triple-negative breast cancer | The data | Finding domains | What is in each domain? | Domains in two tumours | Do the domains differ between kinds of tumour? | Cellular niches in colorectal cancer | Finding niches | Comparing niches between groups of patients | Using your own clustering | Choosing the settings | How it works | Reporting results | Session information | References
Package: lisaClust 1.21.13
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_1.21.13.tar.gz
lisaClust_1.21.13.zip(r-4.7-x86_64)lisaClust_1.21.13.zip(r-4.7-arm64)lisaClust_1.21.13.zip(r-4.6-x86_64)lisaClust_1.21.13.zip(r-4.6-arm64)lisaClust_1.21.13.zip(r-4.5-x86_64)
lisaClust_1.21.13.tgz(r-4.6-x86_64)lisaClust_1.21.13.tgz(r-4.6-arm64)lisaClust_1.21.13.tgz(r-4.5-x86_64)lisaClust_1.21.13.tgz(r-4.5-arm64)
lisaClust_1.21.13.tar.gz(r-4.7-arm64)lisaClust_1.21.13.tar.gz(r-4.7-x86_64)lisaClust_1.21.13.tar.gz(r-4.6-arm64)lisaClust_1.21.13.tar.gz(r-4.6-x86_64)
lisaClust_1.21.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
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-1.21.11(bioc 3.24)lisaClust-1.20.0(bioc 3.23)
singlecellcellbasedassaysspatialcpp
Last updated from:a52849b521. Checks:1 WARNING, 15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 355 | ||
| linux-devel-arm64 | OK | 312 | ||
| linux-devel-x86_64 | OK | 408 | ||
| source / vignettes | OK | 635 | ||
| linux-release-arm64 | OK | 405 | ||
| linux-release-x86_64 | OK | 571 | ||
| macos-release-arm64 | OK | 251 | ||
| macos-release-x86_64 | OK | 542 | ||
| macos-oldrel-arm64 | OK | 303 | ||
| macos-oldrel-x86_64 | OK | 586 | ||
| windows-devel-arm64 | OK | 401 | ||
| windows-devel-x86_64 | OK | 455 | ||
| windows-release-arm64 | OK | 359 | ||
| windows-release-x86_64 | OK | 616 | ||
| windows-oldrel-x86_64 | OK | 417 | ||
| wasm-release | OK | 318 |
Exports:geom_hatchinghatchingPlotinhomLocalKlisalisaClustnameRegionsregionBoxPlotregionMapscale_regionscale_region_manual
Dependencies:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclicodetoolscpp11curlDBIdbplyrDelayedArraydeldirdplyrfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegoftestgtablehttr2IRangesisobandlabelinglambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisenlmeopensslpheatmappillarpkgconfigpolyclippurrrR6RColorBrewerRcppRhpcBLASctlrjsonrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsystensortibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
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 |
| Name regions by the cell types they are enriched for | nameRegions |
| Compare the share of each region between groups | regionBoxPlot |
| Plot heatmap of cell type enrichment for lisaClust regions | regionMap |
| Scale constructor for regions | scale_region scale_region_manual |