├── Compass.R ├── FLOWMAP.R ├── GeneExpressionSignatures ├── ComplexHeatmap.R ├── DESeq2byOrg-paired.R ├── DESeq2signatures-ModuleScores.R ├── DESeq_acrossdatasets_timepts-figure.R ├── ModuleScoreExpression.R └── RRHO.R ├── Harmony.R ├── Plots.R ├── RandomForest ├── Figures_for_pval.R ├── RF_utils.R ├── run_RF_HumanToOrg.R ├── run_RF_OrgToHuman.R └── run_RF_randombackgrounds.R ├── RunAzimuth.R ├── RunDecontX.R ├── SlideSeqAnalysis.R ├── Subclustering.R ├── URD ├── AUCPR_gene_smooth_fit.R ├── URD_driver.sh ├── branching_point_plot.R ├── branchpint_DE.R ├── gradient_boosting_classifier.py ├── run_URD.R └── sort_genes_by_feature_importance.R ├── WGCNA ├── RunWGCNA.R └── choosePowerWGCNA.R ├── cNMF ├── apply_cNMF_modules_seurat.R ├── cNMF.R └── run_cNMF.R ├── initial_seurat.R ├── mutual_information.R └── scATAC analysis ├── DAR.R ├── Motif_figures.R ├── PeaksExclusiveToOrganoids.R ├── RRHO2_scATAC.R ├── peakStats.R └── scATAC.R /Compass.R: 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