├── .Rbuildignore ├── .gitignore ├── CELESTA.Rproj ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R └── CELESTA_functions.R ├── README.Rmd ├── README.md ├── data ├── high_marker_threshold_anchor.rda ├── high_marker_threshold_iteration.rda ├── imaging_data.csv ├── imaging_data.rda ├── low_marker_threshold_anchor.rda ├── low_marker_threshold_iteration.rda ├── prior_marker_info.csv └── prior_marker_info.rda ├── images ├── CD31_threshold.png ├── Cytokeratin_threshold.png ├── aSMA_threshold.png ├── demo_image.png ├── high_threshold_example.png ├── low_threshold_example.png ├── plot_cell_assignment.png ├── prior_matrix_example.png └── segmented_file_example.png ├── man ├── AssignCellTypes.Rd ├── AssignCells.Rd ├── BuildSigmoidFunction.Rd ├── CalcMarkerActivationProbability.Rd ├── CalculateBeta.Rd ├── CalculateIndexCellProb.Rd ├── CalculateProbabilityDifference.Rd ├── CalculateScores.Rd ├── Celesta-class.Rd ├── CountCellType.Rd ├── CreateCelestaObject.Rd ├── FilterArtifactCells.Rd ├── FilterCells.Rd ├── FindCellsToCheck.Rd ├── FindCellsWithId.Rd ├── FitGmmModel.Rd ├── GetCoords.Rd ├── GetDistFromNearestAssignedCells.Rd ├── GetFinalInferredCellTypes.Rd ├── GetInitialPriorMatrix.Rd ├── GetMarkerExpMatrix.Rd ├── GetNeighborInfo.Rd ├── GetPriorInfo.Rd ├── GetScore.Rd ├── InitializeCellAndScoringMatrices.Rd ├── MarkQuestionableCells.Rd ├── NeighborCellType.Rd ├── PlotCellsAnyCombination.Rd ├── PlotExpProb.Rd ├── PlotSingleExpProb.Rd ├── UpdatePriorMatrix.Rd └── figures │ └── README-pressure-1.png └── tests ├── CELESTA_functions_orig.R ├── testthat.R └── testthat ├── project_title_anchor_cell_assignment.csv ├── project_title_final_cell_type_assignment.csv └── test-CELESTA_functions.R /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/plevritis-lab/CELESTA/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: 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