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 |
methods | Get and set methods for Milo objects |
Milo | The Milo constructor |
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 |
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