Man pages for MikeDMorgan/miloR
Differential neighbourhood abundance testing on a graph

annotateNhoodsAdd annotations from colData to DA testing results
buildFromAdjacencyBuild a graph from an input adjacency matrix
buildGraphBuild a k-nearest neighbour graph
buildNhoodGraphBuild an abstracted graph of neighbourhoods for visualization
calcNhoodDistanceCalculate within neighbourhood distances
calcNhoodExpressionAverage expression within neighbourhoods
countCellsCount cells in neighbourhoods
findNhoodGroupMarkersIdentify post-hoc neighbourhood marker genes
findNhoodMarkersIdentify post-hoc neighbourhood marker genes
graphSpatialFDRControl the spatial FDR
groupNhoodsGroup neighbourhoods
makeNhoodsDefine neighbourhoods on a graph (fast)
matrixORMatrix-classThe Milo container class
methodsGet and set methods for Milo objects
MiloThe Milo constructor
miloR-packageThe miloR package
plotDAbeeswarmVisualize DA results as a beeswarm plot
plotNhoodExpressionDAVisualize gene expression in neighbourhoods
plotNhoodGraphPlot graph of neighbourhood
plotNhoodGraphDAPlot Milo results on graph of neighbourhood
plotNhoodMAVisualize DA results as an MAplot
plotNhoodSizeHistPlot histogram of neighbourhood sizes
sim_discretesim_discrete
sim_trajectorySimulated linear trajectory data
testDiffExpPerform post-hoc differential gene expression analysis
testNhoodsPerform differential neighbourhood abundance testing
MikeDMorgan/miloR documentation built on Aug. 7, 2022, 8:21 a.m.