├── .Rbuildignore ├── .github └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE.txt ├── NAMESPACE ├── R ├── RcppExports.R ├── SingleR.R ├── aggregateReference.R ├── classifySingleR.R ├── combineCommonResults.R ├── combineRecomputedResults.R ├── datasets.R ├── getClassicMarkers.R ├── getDeltaFromMedian.R ├── matchReferences.R ├── mockData.R ├── plotDeltaDistribution.R ├── plotMarkerHeatmap.R ├── plotScoreDistribution.R ├── plotScoreHeatmap.R ├── pruneScores.R ├── rebuildIndices.R ├── trainSingleR.R ├── utils.R └── zzz.R ├── README.md ├── inst ├── CITATION └── NEWS.Rd ├── man ├── SingleR.Rd ├── aggregateReference.Rd ├── classifySingleR.Rd ├── combineRecomputedResults.Rd ├── datasets.Rd ├── getClassicMarkers.Rd ├── getDeltaFromMedian.Rd ├── matchReferences.Rd ├── mockData.Rd ├── plotDeltaDistribution.Rd ├── plotMarkerHeatmap.Rd ├── plotScoreDistribution.Rd ├── plotScoreHeatmap.Rd ├── pruneScores.Rd ├── rebuildIndex.Rd └── trainSingleR.Rd ├── src ├── RcppExports.cpp ├── classify_integrated.cpp ├── classify_single.cpp ├── find_classic_markers.cpp ├── grouped_medians.cpp ├── set_executor.cpp ├── train_integrated.cpp ├── train_single.cpp └── utils.h ├── tests ├── testthat.R └── testthat │ ├── setup.R │ ├── test-SingleR.R │ ├── test-aggregate.R │ ├── test-classify.R │ ├── test-heatmap.R │ ├── test-markers.R │ ├── test-plotMarkerHeatmap.R │ ├── test-prune.R │ ├── test-rebuild.R │ ├── test-recomputed.R │ ├── test-score-dist.R │ ├── test-train.R │ └── test-utils.R └── vignettes ├── SingleR.Rmd └── ref.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SingleR-inc/SingleR/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/workflows/check-bioc.yml: -------------------------------------------------------------------------------- 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