Milo-class              The Milo constructor
Milo-methods            Get and set methods for Milo objects
Satterthwaite_df        Compute degrees of freedom using Satterthwaite
                        method
annotateNhoods          Add annotations from colData to DA testing
                        results
buildFromAdjacency      Build a graph from an input adjacency matrix
buildGraph              Build a k-nearest neighbour graph
buildNhoodGraph         Build an abstracted graph of neighbourhoods for
                        visualization
calcNhoodDistance       Calculate within neighbourhood distances
calcNhoodExpression     Average expression within neighbourhoods
checkSeparation         Check for separation of count distributions by
                        variables
computePvalue           Compute the p-value for the fixed effect
                        parameters
countCells              Count cells in neighbourhoods
findNhoodGroupMarkers   Identify post-hoc neighbourhood marker genes
findNhoodMarkers        Identify post-hoc neighbourhood marker genes
fitGLMM                 Perform differential abundance testing using a
                        NB-generalised linear mixed model
fitGeneticPLGlmm        GLMM parameter estimation using
                        pseudo-likelihood with a custom covariance
                        matrix
fitPLGlmm               GLMM parameter estimation using
                        pseudo-likelihood
glmmControl.defaults    glmm control default values
graphSpatialFDR         Control the spatial FDR
groupNhoods             Group neighbourhoods
initialiseG             Construct the initial G matrix
initializeFullZ         Construct the full Z matrix
makeNhoods              Define neighbourhoods on a graph (fast)
matrix.trace            Compute the trace of a matrix
miloR                   miloR
miloR-package           The miloR package
plotDAbeeswarm          Visualize DA results as a beeswarm plot
plotNhoodCounts         Plot the number of cells in a neighbourhood per
                        sample and condition
plotNhoodExpressionDA   Visualize gene expression in neighbourhoods
plotNhoodGraph          Plot graph of neighbourhood
plotNhoodGraphDA        Plot Milo results on graph of neighbourhood
plotNhoodGroups         Plot graph of neighbourhoods coloring by
                        nhoodGroups
plotNhoodMA             Visualize DA results as an MAplot
plotNhoodSizeHist       Plot histogram of neighbourhood sizes
sim_discrete            sim_discrete
sim_family              sim_family
sim_nbglmm              sim_nbglmm
sim_trajectory          Simulated linear trajectory data
testDiffExp             Perform post-hoc differential gene expression
                        analysis
testNhoods              Perform differential neighbourhood abundance
                        testing
