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| miloR-package | The miloR package |
| 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 |
| graph | Get and set methods for Milo objects |
| graph-method | Get and set methods for Milo objects |
| graph<- | Get and set methods for Milo objects |
| graph<--method | Get and set methods for Milo objects |
| graphSpatialFDR | Control the spatial FDR |
| groupNhoods | Group neighbourhoods |
| makeNhoods | Define neighbourhoods on a graph (fast) |
| matrixORMatrix-class | The Milo container class |
| Milo | The Milo constructor |
| Milo-class | The Milo constructor |
| Milo-methods | Get and set methods for Milo objects |
| nhoodAdjacency | Get and set methods for Milo objects |
| nhoodAdjacency-method | Get and set methods for Milo objects |
| nhoodAdjacency<- | Get and set methods for Milo objects |
| nhoodAdjacency<--method | Get and set methods for Milo objects |
| nhoodCounts | Get and set methods for Milo objects |
| nhoodCounts-method | Get and set methods for Milo objects |
| nhoodCounts<- | Get and set methods for Milo objects |
| nhoodCounts<--method | Get and set methods for Milo objects |
| nhoodDistances | Get and set methods for Milo objects |
| nhoodDistances-method | Get and set methods for Milo objects |
| nhoodDistances<- | Get and set methods for Milo objects |
| nhoodDistances<--method | Get and set methods for Milo objects |
| nhoodExpression | Get and set methods for Milo objects |
| nhoodExpression-method | Get and set methods for Milo objects |
| nhoodExpression<- | Get and set methods for Milo objects |
| nhoodExpression<--method | Get and set methods for Milo objects |
| nhoodGraph | Get and set methods for Milo objects |
| nhoodGraph-method | Get and set methods for Milo objects |
| nhoodGraph<- | Get and set methods for Milo objects |
| nhoodGraph<--method | Get and set methods for Milo objects |
| nhoodIndex | Get and set methods for Milo objects |
| nhoodIndex-method | Get and set methods for Milo objects |
| nhoodIndex<- | Get and set methods for Milo objects |
| nhoodIndex<--method | Get and set methods for Milo objects |
| nhoodReducedDim | Get and set methods for Milo objects |
| nhoodReducedDim-method | Get and set methods for Milo objects |
| nhoodReducedDim<- | Get and set methods for Milo objects |
| nhoodReducedDim<--method | Get and set methods for Milo objects |
| nhoods | Get and set methods for Milo objects |
| nhoods-method | Get and set methods for Milo objects |
| nhoods<- | Get and set methods for Milo objects |
| nhoods<--method | Get and set methods for Milo objects |
| plotDAbeeswarm | Visualize DA results as a beeswarm plot |
| plotNhoodExpressionDA | Visualize gene expression in neighbourhoods |
| plotNhoodExpressionGroups | Visualize gene expression in neighbourhoods |
| plotNhoodGraph | Plot graph of neighbourhood |
| plotNhoodGraphDA | Plot Milo results on graph of neighbourhood |
| plotNhoodGroups | Plot Milo results on graph of neighbourhood |
| plotNhoodMA | Visualize DA results as an MAplot |
| plotNhoodSizeHist | Plot histogram of neighbourhood sizes |
| show | Get and set methods for Milo objects |
| show-method | Get and set methods for Milo objects |
| sim_discrete | sim_discrete |
| sim_trajectory | Simulated linear trajectory data |
| testDiffExp | Perform post-hoc differential gene expression analysis |
| testNhoods | Perform differential neighbourhood abundance testing |