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