├── .Rbuildignore ├── .github └── workflows │ └── r-build-check.yml ├── .gitignore ├── .lintr ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── AllGenerics.R ├── allClasses.R ├── alluvialMat.R ├── aucMat.R ├── cluster2pattern.R ├── clusterPlotR.R ├── correlateR.R ├── geneMatchR.R ├── helperFunctions.R ├── intersectoR.R ├── multivariateAnalysisR.R ├── package.R ├── plotting.R ├── projectR.R ├── projectionDriveRfun.R └── rotatoR.R ├── README.md ├── data ├── .Rapp.history ├── AP.RNAseq6l3c3t.RData ├── CR.RNAseq6l3c3t.RData ├── cr_microglial.rda ├── glial_counts.rda ├── map.ESepiGen4c1l.RData ├── map.RNAseq6l3c3t.RData ├── microglial_counts.rda ├── multivariateAnalysisR_seurat_test.RData ├── p.ESepiGen4c1l.RData ├── p.RNAseq6l3c3t.RData ├── pd.ESepiGen4c1l.RData ├── pd.RNAseq6l3c3t.RData └── retinal_patterns.rda ├── inst └── CITATION ├── man ├── AP.RNAseq6l3c3t.Rd ├── CR.RNAseq6l3c3t.Rd ├── alluvialMat.Rd ├── aucMat.Rd ├── bonferroniCorrectedDifferences.Rd ├── cluster2pattern-class.Rd ├── cluster2pattern-methods.Rd ├── clusterPlotR-methods.Rd ├── correlateR-class.Rd ├── correlateR.Rd ├── cr_microglial.Rd ├── geneMatchR.Rd ├── getTSNE.Rd ├── getUMAP.Rd ├── glial_counts.Rd ├── initialize-cluster2pattern-method.Rd ├── initialize-correlateR-method.Rd ├── initialize-rotatoR-method.Rd ├── intersectoR-methods.Rd ├── map.ESepiGen4c1l.Rd ├── map.RNAseq6l3c3t.Rd ├── microglial_counts.Rd ├── multivariateAnalysisR.Rd ├── multivariateAnalysisR_seurat_test.Rd ├── p.ESepiGen4c1l.Rd ├── p.RNAseq6l3c3t.Rd ├── pd.ESepiGen4c1l.Rd ├── pd.RNAseq6l3c3t.Rd ├── pdVolcano.Rd ├── plotConfidenceIntervals.Rd ├── plotVolcano.Rd ├── projectR-methods.Rd ├── projectionDriveR.Rd ├── retinal_patterns.Rd ├── rotatoR-class.Rd └── rotatoR.Rd ├── tests ├── testthat.R └── testthat │ └── test_projectR.R └── vignettes ├── projectR.Rmd ├── projectR.bib ├── projectR.html └── projectR.tex /.Rbuildignore: -------------------------------------------------------------------------------- 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