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.
Last updated 29 days ago
singlecellcellbasedassaysspatial
8 stars 7.92 score 162 dependencies 1 dependentslisaClust - 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.
Last updated 2 months ago
singlecellcellbasedassaysspatial
3 stars 6.15 score 164 dependenciessimpleSeg - A package to perform simple cell segmentation
Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.
Last updated 5 months ago
classificationsurvivalsinglecellnormalizationspatialspatial-statistics
1 stars 5.04 score 142 dependencies