Changes in version 1.5.0 - Introduce plotting function to visualise neighbourhood count distributions for nhoods interest: plotNhoodCounts. Implemented by Nick Hirschmüller Changes in version 1.3.1 (2022-01-07) - Fix bug in findNhoodGroupMarkers to merge on gene IDs explicitly - Fix bug in makeNhoods to include index cell in nhoods() matrix - Introduce graph-based neighbourhood definition - allows full compatibility with graph-only batch correction and graphs constructed by third-party tools - Introduce graph-based spatial FDR correction to obviate the need for any distance calculations - Add vignette to describe the use and application of contrasts in testNhoods - Patch to correct SpatialFDR with sparse nhoods where density is ~0 Changes in version 1.1.0 (2021-10-12) - Fix bug in testNhoods to use user-specific reduced dimensions - Vignettes now include set rownames() to avoid confusion - Numerous doc-string typo fixes Changes in version 0.99.1 (2021-03-13) - Fix model normalisation bug - now using TMM normalisation by default. Log(M_s) offset can be used by passing norm.method="logMS" to testNhoods. Changes in version 0.99.0 (2021-03-04) - Submitted to Bioconductor