API for MikeDMorgan/miloR
Differential neighbourhood abundance testing on a graph
| Global functions | |
|---|---|
| .aggregate_dists | Source code |
| .aggregate_dists.hard | Source code |
| .buildGraph | Source code |
| .build_nhood_adjacency | Source code |
| .calc_distance | Source code |
| .calc_expression | Source code |
| .check_binary | Source code |
| .check_empty | Source code |
| .emptyMilo | Source code |
| .fromMatrix | Source code |
| .fromSCE | Source code |
| .graph_refined_sampling | Source code |
| .group_nhoods_by_overlap | Source code |
| .group_nhoods_from_adjacency | Source code |
| .milo_show | Source code |
| .neighborsToKNNGraph | Source code |
| .parse_formula | Source code |
| .perform_counts_dge | Source code |
| .perform_lognormal_dge | Source code |
| .rEParse | Source code |
| .refined_sampling | Source code |
| .sample_vertices | Source code |
| .set_reduced_dims | Source code |
| .setup_knn_data | Source code |
| .valid_graph | Source code |
| .valid_nhood | Source code |
| Milo | Man page Source code |
| Milo-class | Man page |
| Milo-methods | Man page |
| Satterthwaite_df | Man page Source code |
| annotateNhoods | Man page Source code |
| buildFromAdjacency | Man page Source code |
| buildGraph | Man page Source code |
| buildNhoodGraph | Man page Source code |
| calcNhoodDistance | Man page Source code |
| calcNhoodExpression | Man page Source code |
| checkSeparation | Man page Source code |
| computePvalue | Man page Source code |
| countCells | Man page Source code |
| findNhoodGroupMarkers | Man page Source code |
| findNhoodMarkers | Man page Source code |
| fitGLMM | Man page Source code |
| fitGeneticPLGlmm | Man page Source code |
| fitPLGlmm | Man page Source code |
| function_jac | Source code |
| glmmControl.defaults | Man page Source code |
| graph | Man page |
| graph,Milo-method | Man page |
| graph<- | Man page |
| graph<-,Milo-method | Man page |
| graphSpatialFDR | Man page Source code |
| groupNhoods | Man page Source code |
| initialiseG | Man page Source code |
| initializeFullZ | Man page Source code |
| makeNhoods | Man page Source code |
| matrix.trace | Man page Source code |
| miloR | Man page |
| miloR-package | Man page |
| nhoodAdjacency | Man page |
| nhoodAdjacency,Milo-method | Man page |
| nhoodAdjacency<- | Man page |
| nhoodAdjacency<-,Milo-method | Man page |
| nhoodCounts | Man page |
| nhoodCounts,Milo-method | Man page |
| nhoodCounts<- | Man page |
| nhoodCounts<-,Milo-method | Man page |
| nhoodDistances | Man page |
| nhoodDistances,Milo-method | Man page |
| nhoodDistances<- | Man page |
| nhoodDistances<-,Milo-method | Man page |
| nhoodExpression | Man page |
| nhoodExpression,Milo-method | Man page |
| nhoodExpression<- | Man page |
| nhoodExpression<-,Milo-method | Man page |
| nhoodGraph | Man page |
| nhoodGraph,Milo-method | Man page |
| nhoodGraph<- | Man page |
| nhoodGraph<-,Milo-method | Man page |
| nhoodIndex | Man page |
| nhoodIndex,Milo-method | Man page |
| nhoodIndex<- | Man page |
| nhoodIndex<-,Milo-method | Man page |
| nhoodReducedDim | Man page |
| nhoodReducedDim,Milo-method | Man page |
| nhoodReducedDim<- | Man page |
| nhoodReducedDim<-,Milo-method | Man page |
| nhoods | Man page |
| nhoods,Milo-method | Man page |
| nhoods<- | Man page |
| nhoods<-,Milo-method | Man page |
| plotDAbeeswarm | Man page |
| plotNhoodCounts | Man page |
| plotNhoodExpressionDA | Man page Source code |
| plotNhoodExpressionGroups | Man page |
| plotNhoodGraph | Man page Source code |
| plotNhoodGraphDA | Man page Source code |
| plotNhoodGroups | Man page Source code |
| plotNhoodMA | Man page |
| plotNhoodSizeHist | Man page Source code |
| show | Man page |
| show,Milo-method | Man page |
| sim_discrete | Man page |
| sim_family | Man page |
| sim_nbglmm | Man page |
| sim_trajectory | Man page |
| testDiffExp | Man page Source code |
| testNhoods | Man page Source code |
