Changelog

spatialGE 1.2.1

  • Added C++ code to speed up STenrich computations (Thank you, Dr. Soupir!).
  • The STenrich function can now calculate gene set enrichment scores (via GSVA) in addition to gene set average expression.
  • The STenrich function can now test for gene set “hot-spots” within an specific tissue domain (annot and domain arguments).
  • Spatial distances can now be log-transformed for STgradient (log argument).
  • Example data sets are now in the spatialGE_Data GitHub repository.
  • New functions spatial_metadata and tissue_names to quickly access the names of spot/cell annotations and sample names.
  • Re-assessed package dependencies.
  • Use of DelayedArray for some calculations.
  • Several bug fixes.

spatialGE 1.2.0

  • Functions STenrich, STgradient, and STdiff available.
  • Added C++ code for Seurat’s implementation of FindVariableFeatures

spatialGE 1.1.0

  • Multiple, significant changes to STlist (incompatible with STlist objects from version 1.0).