Milo-class              The Milo constructor
Milo-methods            Get and set methods for Milo objects
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
countCells              Count cells in neighbourhoods
findNhoodGroupMarkers   Identify post-hoc neighbourhood marker genes
findNhoodMarkers        Identify post-hoc neighbourhood marker genes
graphSpatialFDR         Control the spatial FDR
groupNhoods             Group neighbourhoods
makeNhoods              Define neighbourhoods on a graph (fast)
matrixORMatrix-class    The Milo container class
miloR-package           The miloR package
plotDAbeeswarm          Visualize DA results as a beeswarm plot
plotNhoodExpressionDA   Visualize gene expression in neighbourhoods
plotNhoodGraph          Plot graph of neighbourhood
plotNhoodGraphDA        Plot Milo results on graph of neighbourhood
plotNhoodMA             Visualize DA results as an MAplot
plotNhoodSizeHist       Plot histogram of neighbourhood sizes
sim_discrete            sim_discrete
sim_trajectory          Simulated linear trajectory data
testDiffExp             Perform post-hoc differential gene expression
                        analysis
testNhoods              Perform differential neighbourhood abundance
                        testing
