├── .github └── workflows │ └── main.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── TIL_barplot.R ├── algorithm2.R ├── collapseCellTypes.R ├── convertCellScoresToCounts.R ├── convertCellTypes.R ├── create_profile_matrix.R ├── data.R ├── deconLNR.R ├── deriveWeights.R ├── derive_GeoMx_background.R ├── download_profile_matrix.R ├── flagOutliers.R ├── florets.R ├── mergeTumorIntoX.R ├── package.R ├── reverseDecon.R ├── runCollapseCellTypes.R ├── runErrorModel.R ├── runmergeTumorIntoXGeo.R ├── runreverseDeconGeo.R ├── runspatialdecon.R └── spatialdecon.R ├── README.md ├── data ├── cellcols.RData ├── mean.resid.sd.RData ├── mini_geomx_dataset.RData ├── mini_singleCell_dataset.RData ├── nsclc.RData ├── safeTME.RData └── safeTME.matches.RData ├── man ├── SpatialDecon-package.Rd ├── TIL_barplot.Rd ├── cellcols.Rd ├── collapseCellTypes.Rd ├── create_profile_matrix.Rd ├── derive_GeoMx_background.Rd ├── download_profile_matrix.Rd ├── florets.Rd ├── mean.resid.sd.Rd ├── mergeTumorIntoX.Rd ├── mini_geomx_dataset.Rd ├── mini_singleCell_dataset.Rd ├── nsclc.Rd ├── reverseDecon.Rd ├── runCollapseCellTypes.Rd ├── runErrorModel.Rd ├── runMergeTumorIntoX.Rd ├── runReverseDecon.Rd ├── runspatialdecon.Rd ├── safeTME.Rd ├── safeTME.matches.Rd └── spatialdecon.Rd ├── tests ├── testthat.R └── testthat │ ├── expectedtestresults.RData │ ├── test-integration-testing.R │ └── testdata.RData └── vignettes ├── SpatialDecon_vignette.Rmd └── SpatialDecon_vignette_NSCLC.Rmd /.github/workflows/main.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/SpatialDecon/HEAD/.github/workflows/main.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/SpatialDecon/HEAD/.gitignore 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