Changes in version 2.0.1 (2024-04-30)                  

  - Introduce NB-GLMM into Milo 2.0 for random effect variables and
    modelling dependencies between observations
  - Diagnostic function for checking model separation for experimental
    variables, i.e. splitting zero from non-zero counts perfectly
  - Vignette describing basic usage of GLMM functions in testNhoods

                  Changes in version 2.0 (2024-10-30)                   

  - Warning on GLMM if glmm.solver not set
  - Bug fix in model contrasts vignette with multiple contrasts
  - testNhoods will error if N<60 and using GLMM - introduce force=TRUE
    to override (with a warning)
  - DA nhoods can be emphasised in plotNhoodGraphDA with highlight.da

                  Changes in version 1.60 (2022-11-02)                  

  - Vignette describing the use of contrasts in testNhoods

                 Changes in version 1.7.1 (2023-02-15)                  

  - Patch to fix NA plotting in plotDABeeswarm

                 Changes in version 1.5.0 (2022-04-27)                  

  - 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