Package: lisaClust 1.13.1

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]

lisaClust_1.13.1.tar.gz
lisaClust_1.13.1.zip(r-4.5)lisaClust_1.13.1.zip(r-4.4)lisaClust_1.13.1.zip(r-4.3)
lisaClust_1.13.1.tgz(r-4.4-any)lisaClust_1.13.1.tgz(r-4.3-any)
lisaClust_1.13.1.tar.gz(r-4.5-noble)lisaClust_1.13.1.tar.gz(r-4.4-noble)
lisaClust_1.13.1.tgz(r-4.4-emscripten)lisaClust_1.13.1.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-1.13.0(bioc 3.20)lisaClust-1.12.0(bioc 3.19)

bioconductor-package

8 exports 1.00 score 171 dependencies

Last updated 29 days agofrom:539d46c756

Exports:geom_hatching hatchingPlot inhomLocalK lisa lisaClust regionMap scale_region scale_region_manual

Dependencies:abind annotate AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocParallel Biostrings bit bit64 blob boot brio broom cachem callr car carData class ClassifyR classInt cli codetools colorspace concaveman corrplot cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir desc diffobj digest dplyr e1071 evaluate fansi farver fastmap filelock formatR fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggplot2 ggpubr ggrepel ggsci ggsignif ggupset glue goftest gridExtra gtable httr IRanges isoband jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle lme4 lmerTest magick magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa MultiAssayExperiment munsell nlme nloptr nnet numDeriv openssl pbkrtest pheatmap pillar pkgbuild pkgconfig pkgload plogr plyr png polyclip polynom praise processx proxy ps purrr quantreg R6 ranger RColorBrewer Rcpp RcppEigen rematch2 reshape2 rjson rlang rprojroot RSQLite rstatix s2 S4Arrays S4Vectors scales scam sf SingleCellExperiment snow SparseArray SparseM SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.utils spicyR stringi stringr SummarizedExperiment survival sys systemfonts tensor testthat tibble tidyr tidyselect tweenr UCSC.utils units utf8 V8 vctrs viridisLite waldo withr wk XML xtable XVector zlibbioc

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

Nicolas Canete, Ellis Patrick

Rendered fromlisaClust.Rmdusingknitr::rmarkdownon Jun 13 2024.

Last update: 2024-06-12
Started: 2021-03-15

Citation

Development and contributors

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