Package: spicyR 1.17.1

Ellis Patrick

spicyR: Spatial analysis of in situ cytometry data

The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.

Authors:Nicolas Canete [aut], Ellis Patrick [aut, cre], Nicholas Robertson [ctb]

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spicyR.pdf |spicyR.html✨
spicyR/json (API)

# Install 'spicyR' in R:

install.packages('spicyR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sydneybiox/spicyr/issues

Datasets:

diabetesData - Diabetes IMC data in SCE format.
spicyTest - Results from spicy for diabetesData

On BioConductor:spicyR-1.17.1(bioc 3.20)spicyR-1.16.1(bioc 3.19)

bioconductor-package

9 exports 2.18 score 154 dependencies 1 dependents

Last updated 2 months agofrom:94657baa09

Exports:bind colTest convPairs getPairwise getProp signifPlot spicy spicyBoxPlot topPairs

Dependencies:abind annotate AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocParallel Biostrings bit bit64 blob boot broom cachem car carData class ClassifyR classInt cli codetools colorspace concaveman corrplot cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dplyr e1071 fansi farver fastmap filelock formatR 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 pkgconfig plogr plyr png polyclip polynom proxy purrr quantreg R6 ranger RColorBrewer Rcpp RcppEigen reshape2 rjson rlang 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 stringi stringr SummarizedExperiment survival sys systemfonts tensor tibble tidyr tidyselect tweenr UCSC.utils units utf8 V8 vctrs viridisLite withr wk XML xtable XVector zlibbioc

Spatial Mixed-Effects Modelling with spicy

Nicolas Canete, Ellis Patrick

Rendered fromspicyR.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2024-05-20
Started: 2022-11-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Produces a dataframe showing L-function metric for each imageID entry.	bind
Perform a simple wilcoxon-rank-sum test or t-test on the columns of a data frame	colTest
Converts colPairs object into an abundance matrix based on number of nearby interactions for every cell type.	convPairs
Diabetes IMC data in SCE format.	diabetesData
Get statistic from pairwise L curve of a single image.	getPairwise
Get proportions from a SummarizedExperiment.	getProp
Plots result of signifPlot.	signifPlot
Plots boxplot for a specified cell-cell relationship	spicyBoxPlot
Performs spatial tests on spatial cytometry data.	spicy spicy,spicy-method SpicyResults,list,ANY-method SpicyResults-class
Results from spicy for diabetesData	spicyTest
A table of the significant results from spicy tests	topPairs topPairs,SpicyResults-method