Package: lisaClust 1.21.0

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_1.21.0.tar.gz
lisaClust_1.21.0.zip(r-4.7)lisaClust_1.21.0.zip(r-4.6)lisaClust_1.21.0.zip(r-4.5)
lisaClust_1.21.0.tgz(r-4.6-any)lisaClust_1.21.0.tgz(r-4.5-any)
lisaClust_1.21.0.tar.gz(r-4.7-any)lisaClust_1.21.0.tar.gz(r-4.6-any)
lisaClust_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
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-1.21.0(bioc 3.24)lisaClust-1.20.0(bioc 3.23)

singlecell cellbasedassays spatial

6.19 score 4 stars 55 scripts 8 exports 232 dependencies

Last updated from:144e9d12a8. Checks:1 WARNING, 6 NOTE, 2 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	236
linux-devel-x86_64	NOTE	480
source / vignettes	OK	465
linux-release-x86_64	NOTE	464
macos-release-arm64	ERROR	197
macos-oldrel-arm64	NOTE	257
windows-devel	NOTE	412
windows-release	NOTE	395
windows-oldrel	NOTE	442
wasm-release	OK	268

Exports:geom_hatching hatchingPlot inhomLocalK lisa lisaClust regionMap scale_region scale_region_manual

Dependencies:abind annotate AnnotationDbi askpass backports base64enc bdsmatrix beeswarm BH Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocParallel Biostrings bit bit64 bitops blob boot broom bslib cachem car carData circlize class ClassifyR classInt cli codetools colorspace commonmark concaveman corrplot cowplot coxme cpp11 crayon curl cytomapper data.table DBI dbplyr dcanr DelayedArray deldir Deriv digest dir.expiry doBy doRNG dplyr e1071 EBImage evaluate farver fastmap fftwtools filelock fontawesome foreach forecast formatR Formula fracdiff fs futile.logger futile.options genefilter generics GenomicRanges ggbeeswarm ggforce ggh4x ggnewscale ggplot2 ggpubr ggrepel ggsci ggsignif ggthemes ggupset GlobalOptions glue goftest gridExtra gtable h5mread HDF5Array highr htmltools htmlwidgets httpuv httr httr2 igraph IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lifecycle lme4 lmerTest lmtest locfit magick magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr MultiAssayExperiment nlme nloptr nnet nnls numDeriv openssl otel pbkrtest pheatmap pillar pkgconfig plyr png polyclip polynom promises proxy purrr quantreg R6 ranger rappdirs raster rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas reshape2 rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown rngtools RSQLite rstatix s2 S4Arrays S4Vectors S7 sass scales scam Seqinfo sf shape shiny shinydashboard simpleSeg SingleCellExperiment snow sourcetools sp SparseArray SparseM SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils spicyR stringi stringr SummarizedExperiment survival svglite svgPanZoom sys systemfonts tensor terra textshaping tibble tidyr tidyselect tiff timeDate tinytex tweenr units urca utf8 V8 vctrs vipor viridis viridisLite withr wk xfun XML xtable XVector yaml zoo

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

Rendered fromlisaClust.Rmdusingknitr::rmarkdown

Last update: 2024-10-08
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