Spatial analysis of in situ cytometry data

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Documentation for package ‘spicyR’ version 1.16.1

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