├── .Rbuildignore ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ └── RCMD_check.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── NEWS.md ├── R ├── AllClasses.R ├── AllGenerics.R ├── RcppExports.R ├── annotateNhoods.R ├── buildFromAdjacency.R ├── buildGraph.R ├── buildNhoodGraph.R ├── calcNhoodDistance.R ├── calcNhoodExpression.R ├── checkSeparation.R ├── countCells.R ├── findNhoodGroupMarkers.R ├── findNhoodMarkers.R ├── glmm.R ├── graphSpatialFDR.R ├── groupNhoods.R ├── makeNhoods.R ├── methods.R ├── milo.R ├── miloR-package.R ├── miloR.R ├── plotNhoods.R ├── sim_discrete.R ├── sim_family.R ├── sim_nbglmm.R ├── sim_trajectory.R ├── testDiffExp.R ├── testNhoods.R └── utils.R ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── data ├── sim_discrete.RData ├── sim_family.RData ├── sim_nbglmm.RData └── sim_trajectory.RData ├── docs ├── 404.html ├── articles │ ├── index.html │ ├── milo_demo.html │ ├── milo_demo_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ ├── figure-html │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ └── header-attrs-2.3 │ │ │ └── header-attrs.js │ ├── milo_gastrulation.html │ └── milo_gastrulation_files │ │ ├── accessible-code-block-0.0.1 │ │ └── empty-anchor.js │ │ ├── figure-html │ │ ├── unnamed-chunk-14-1.png │ │ ├── unnamed-chunk-15-1.png │ │ ├── unnamed-chunk-16-1.png │ │ ├── unnamed-chunk-18-1.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-22-1.png │ │ ├── unnamed-chunk-3-1.png │ │ └── unnamed-chunk-7-1.png │ │ └── header-attrs-2.3 │ │ └── header-attrs.js ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── milo_schematic.png ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── Milo.html │ ├── annotateNhoods.html │ ├── buildFromAdjacency.html │ ├── buildGraph.html │ ├── buildNhoodGraph.html │ ├── calcNhoodDistance.html │ ├── calcNhoodExpression.html │ ├── countCells.html │ ├── findNhoodMarkers.html │ ├── graphSpatialFDR.html │ ├── index.html │ ├── makeNhoods.html │ ├── matrixORMatrix-class.html │ ├── methods.html │ ├── plotDAbeeswarm.html │ ├── plotNhoodExpressionDA.html │ ├── plotNhoodGraph.html │ ├── plotNhoodGraphDA.html │ ├── plotNhoodSizeHist-1.png │ ├── plotNhoodSizeHist.html │ ├── sim_discrete.html │ ├── sim_trajectory.html │ ├── testDiffExp.html │ └── testNhoods.html ├── man ├── Milo.Rd ├── Satterthwaite_df.Rd ├── annotateNhoods.Rd ├── buildFromAdjacency.Rd ├── buildGraph.Rd ├── buildNhoodGraph.Rd ├── calcNhoodDistance.Rd ├── calcNhoodExpression.Rd ├── checkSeparation.Rd ├── computePvalue.Rd ├── countCells.Rd ├── findNhoodGroupMarkers.Rd ├── findNhoodMarkers.Rd ├── fitGLMM.Rd ├── fitGeneticPLGlmm.Rd ├── fitPLGlmm.Rd ├── glmmControl.defaults.Rd ├── graphSpatialFDR.Rd ├── groupNhoods.Rd ├── initialiseG.Rd ├── initializeFullZ.Rd ├── makeNhoods.Rd ├── matrix.trace.Rd ├── methods.Rd ├── miloR-package.Rd ├── miloR.Rd ├── plotDAbeeswarm.Rd ├── plotNhoodCounts.Rd ├── plotNhoodExpressionDA.Rd ├── plotNhoodGraph.Rd ├── plotNhoodGraphDA.Rd ├── plotNhoodGroups.Rd ├── plotNhoodMA.Rd ├── plotNhoodSizeHist.Rd ├── sim_discrete.Rd ├── sim_family.Rd ├── sim_nbglmm.Rd ├── sim_trajectory.Rd ├── testDiffExp.Rd └── testNhoods.Rd ├── miloR.R ├── miloR_sticker.png ├── milo_schematic.png ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── computeMatrices.cpp ├── computeMatrices.h ├── fitGeneticPLGlmm.cpp ├── fitPLGlmm.cpp ├── inference.cpp ├── inference.h ├── invertPseudoVar.cpp ├── invertPseudoVar.h ├── multiP.cpp ├── multiP.h ├── paramEst.cpp ├── paramEst.h ├── pseudovarPartial.cpp ├── pseudovarPartial.h ├── solveQP.cpp ├── solveQP.h ├── utils.cpp └── utils.h ├── tests ├── testthat.R └── testthat │ ├── test_annotateNhoods.R │ ├── test_buildFromAdjacency.R │ ├── test_buildGraph.R │ ├── test_buildNhoodGraph.R │ ├── test_calcNhoodDistance.R │ ├── 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