2.0.X (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

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

1.7.1 (2023-02-15)

Patch to fix NA plotting in plotDABeeswarm

1.60 (2022-11-02)

Vignette describing the use of contrasts in testNhoods

1.5.0 (2022-04-27)

Introduce plotting function to visualise neighbourhood count distributions for nhoods interest: plotNhoodCounts. Implemented by Nick Hirschmüller

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

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

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.

0.99.0 (2021-03-04)

Submitted to Bioconductor