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spatialFDA - A Tool for Spatial Multi-sample Comparisons

spatialFDA is a package to calculate spatial statistics metrics. The package takes a SpatialExperiment object and calculates spatial statistics metrics using the package spatstat. Then it compares the resulting functions across samples/conditions using functional additive models as implemented in the package refund. Furthermore, it provides exploratory visualisations using functional principal component analysis, as well implemented in refund.

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softwarespatialtranscriptomics

5.93 score 9 stars 1 dependents 35 scripts 335 downloads

multipointR - A package to compare intensities of point patterns across samples with spatial parametric models

`multipointR` is a package to compare the distribution of cells in an image or cross images with point process models. On a single image level point process models (`ppm`) model the spatial distribution of a cell type point pattern as a function of spatial covariates while accounting for natural spacing of cells. The main model class considered in `multipointR` are inhomgoeneous Gibb's point process models. Across multiple images, users can either compare multiple univariate `ppm` models in a for loop or fit one joint model across all images with `mppm`. `multipointR` provides an interface between `SpatialExperiment` and `SpatialFeatureExperiment` objects and let's users flexibly define their own `ppm`/`mppm` models with R's formula interface.

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softwarespatialtranscriptomicssinglecell

4.93 score 1 stars 1 scripts 469 downloads