├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── check-standard.yaml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── MERingue-package.R ├── RcppExports.R ├── app.R ├── cluster.R ├── correlationStatistics.R ├── data.R ├── external.R ├── main.R ├── nearestNeighbor.R ├── parameterChoice.R ├── plot.R ├── process.R └── tsm.R ├── README.md ├── data ├── BCL.rda ├── drosophila.rda ├── mOB.rda ├── mPOA.rda ├── mouseCoronal.rda ├── purkinje.rda └── receptorLigandInfo.rda ├── docs ├── BCL_analysis.md ├── BCL_analysis_files │ └── figure-markdown_strict │ │ ├── bcl-clean-1.png │ │ ├── bcl-inconsistent-1.png │ │ ├── bcl-indsection-1.png │ │ ├── bcl-init-1.png │ │ ├── bcl-sample-1.png │ │ └── bcl-sample-2.png ├── README.md ├── _config.yml ├── _layouts │ └── default.html ├── assets │ ├── css │ │ └── style.scss │ ├── fonts │ │ ├── Noto-Sans-700 │ │ │ ├── Noto-Sans-700.eot │ │ │ ├── Noto-Sans-700.svg │ │ │ ├── Noto-Sans-700.ttf │ │ │ ├── Noto-Sans-700.woff │ │ │ └── Noto-Sans-700.woff2 │ │ ├── Noto-Sans-700italic │ │ │ ├── Noto-Sans-700italic.eot │ │ │ ├── Noto-Sans-700italic.svg │ │ │ ├── Noto-Sans-700italic.ttf │ │ │ ├── Noto-Sans-700italic.woff │ │ │ └── Noto-Sans-700italic.woff2 │ │ ├── Noto-Sans-italic │ │ │ ├── Noto-Sans-italic.eot │ │ │ ├── Noto-Sans-italic.svg │ │ │ ├── Noto-Sans-italic.ttf │ │ │ ├── Noto-Sans-italic.woff │ │ │ └── Noto-Sans-italic.woff2 │ │ └── Noto-Sans-regular │ │ │ ├── Noto-Sans-regular.eot │ │ │ ├── Noto-Sans-regular.svg │ │ │ ├── Noto-Sans-regular.ttf │ │ │ ├── Noto-Sans-regular.woff │ │ │ └── Noto-Sans-regular.woff2 │ ├── img │ │ ├── logo.png │ │ ├── meringue_overview.png │ │ └── meringue_sample.png │ └── js │ │ └── scale.fix.js ├── drosophila_3D_analysis.md ├── drosophila_3D_analysis_files │ └── figure-markdown_strict │ │ ├── drosophila-data-1.png │ │ ├── drosophila-pattern-1.png │ │ ├── drosophila-scc-1.png │ │ └── drosophila-sub-1.png ├── favicon.ico ├── img │ └── meringue_logo.png ├── index.md ├── mOB_analysis.md ├── mOB_analysis_files │ └── figure-markdown_strict │ │ ├── mob-comparison-1.png │ │ ├── mob-diff-gexp-plot-1.png │ │ ├── mob-qc-1.png │ │ ├── mob-spatial-heatmap-1.png │ │ ├── mob-spatial-patterns2-1.png │ │ ├── mob-spatially-cross-cor-1.png │ │ ├── mob-spatially-unaware-1.png │ │ ├── spatial-sub-network-1.png │ │ └── spatial-weights-1.png ├── simulation.md ├── simulation_files │ └── figure-markdown_strict │ │ ├── s1-1.png │ │ ├── s11-1.png │ │ ├── s12-1.png │ │ ├── s12-2.png │ │ ├── s2-1.png │ │ ├── s21-1.png │ │ ├── s22-1.png │ │ ├── s23-1.png │ │ ├── s24-1.png │ │ ├── s24-2.png │ │ ├── s31-1.png │ │ ├── s32-1.png │ │ ├── s33-1.png │ │ └── sim-1.png ├── spatial_clustering.md └── spatial_clustering_files │ └── figure-markdown_strict │ ├── cluster-1.png │ ├── cluster2-1.png │ ├── simulation-pos-1.png │ ├── simulation-trans-1.png │ ├── simulation-trans2-1.png │ ├── spatcluster-1.png │ ├── spatcluster-2.png │ └── spatcluster-3.png ├── inst └── CITATION ├── man ├── BCL.Rd ├── MERINGUE.Rd ├── cleanCounts.Rd ├── drosophila.Rd ├── filterSpatialPatterns.Rd ├── getBnn.Rd ├── getClusters.Rd ├── getCrossLayerNeighbors.Rd ├── getDifferentialGenes.Rd ├── getInterCellTypeWeight.Rd ├── getKnn.Rd ├── getMnn.Rd ├── getOverdispersedGenes.Rd ├── getPv.Rd ├── getSpatialNeighbors.Rd ├── getSpatialPatterns.Rd ├── getSpatiallyInformedClusters.Rd ├── groupSigSpatialPatterns.Rd ├── interCellTypeSpatialCrossCor.Rd ├── interpolate.Rd ├── lisaTest.Rd ├── mOB.Rd ├── mPOA.Rd ├── makeApp.Rd ├── moranPermutationTest.Rd ├── moranTest.Rd ├── moranTest_DEPRECATED.Rd ├── mouseCoronal.Rd ├── normalizeCounts.Rd ├── plotEmbedding.Rd ├── plotInterCellTypeSpatialCrossCor.Rd ├── plotNetwork.Rd ├── plotNetwork3D.Rd ├── purkinje.Rd ├── receptorLigandInfo.Rd ├── rotatePos.Rd ├── signedLisa.Rd ├── signedLisaPlot.Rd ├── spatialCrossCor.Rd ├── spatialCrossCorMatrix.Rd ├── spatialCrossCorTest.Rd ├── spatialCrossCorTorTest.Rd └── winsorize.Rd ├── src ├── MERingue.so ├── 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