NEWS

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miloR 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

miloR 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

miloR 1.60 (2022-11-02)

• Vignette describing the use of contrasts in testNhoods

miloR 1.7.1 (2023-02-15)

• Patch to fix NA plotting in plotDABeeswarm

miloR 1.5.0 (2022-04-27)

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

miloR 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

miloR 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

miloR 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.

miloR 0.99.0 (2021-03-04)

• Submitted to Bioconductor