- Added
findAllHotspots
to use withgetPairwiseInteractingGenes
- Return empty interacting genes list instead of failing with error when no genes pass fdr threshold.
- Updated SpaceMarkersMetric by fixing signage and log transformed to scale magnitude
- Added getSpatialParamsExternal which enables getting spatial parameters from file or from the user.
- Deprecated getSpatialParameters
- Enabled includeSelf = TRUE in getInteractingGenes.R to improve hotspot detection
- Enabled load10XCoords to read coordinates from VisiumHD directory
- Optimized the long running row.dunn.test() function
- Corrected sparse -> dense conversions
- Added getPairwiseInteractingGenes which enables pairwise analysis of interacting patterns
getSpatialFeatures
: add default method to infer the object passed to it.
- Added a
NEWS.md
file to track changes to the package.