├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── marker_based.R ├── reference_based.R ├── simulation.R └── utils.R ├── README.md ├── man ├── CalculateSCCellProportions.Rd ├── CorTri.Rd ├── CountsToCPM.Rd ├── EstimatePCACellTypeProportions.Rd ├── FilterUnexpressedGenes.Rd ├── FilterZeroVarianceGenes.Rd ├── GenerateSCReference.Rd ├── GetCTP.Rd ├── GetNumGenes.Rd ├── GetNumGenesWeighted.Rd ├── GetOverlappingGenes.Rd ├── GetOverlappingSamples.Rd ├── GetUniqueMarkers.Rd ├── MarkerBasedDecomposition.Rd ├── ReferenceBasedDecomposition.Rd ├── SemisupervisedTransformBulk.Rd ├── SeuratToExpressionSet.Rd ├── SimulateBarcode.Rd ├── SimulateData.Rd └── SupervisedTransformBulk.Rd ├── tests ├── testthat.R └── testthat │ ├── test_marker_based.R │ ├── test_ref_based.R │ ├── test_sim.R │ └── test_utils.R └── vignettes ├── .gitignore └── bisque.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 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