├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── AllClasses.R ├── AllGenerics.R ├── DualSubset-methods.R ├── LEM-getset.R ├── LEM-other.R ├── SEBC-methods.R ├── SingleCellExperiment.R ├── altExps.R ├── applySCE.R ├── assays.R ├── colLabels.R ├── colPairs.R ├── combine.R ├── defunct.R ├── internals.R ├── miscellaneous.R ├── namespace.R ├── reduced.dim.matrix.R ├── reducedDims.R ├── rowPairs.R ├── rowSubset.R ├── simplifyToSCE.R ├── sizeFactors.R ├── splitAltExps.R ├── subset.R ├── swapAltExp.R ├── unsplitAltExps.R ├── updateObject.R ├── utils.R └── validity.R ├── README.md ├── SingleCellExperiment.Rproj ├── inst ├── CITATION └── NEWS.Rd ├── man ├── LEM-combine.Rd ├── LEM-getset.Rd ├── LEM-misc.Rd ├── LEM-subset.Rd ├── LinearEmbeddingMatrix.Rd ├── SingleCellExperiment.Rd ├── altExps.Rd ├── applySCE.Rd ├── assays.Rd ├── colLabels.Rd ├── colPairs.Rd ├── combine.Rd ├── defunct.Rd ├── internals.Rd ├── miscellaneous.Rd ├── reduced.dim.matrix.Rd ├── reducedDims.Rd ├── rowPairs.Rd ├── rowSubset.Rd ├── simplifyToSCE.Rd ├── sizeFactors.Rd ├── splitAltExps.Rd ├── swapAltExp.Rd ├── unsplitAltExps.Rd └── updateObject.Rd ├── tests ├── testthat.R └── testthat │ ├── setup.R │ ├── test-DualSubset.R │ ├── test-applySCE.R │ ├── test-colPairs.R │ ├── test-lem-class.R │ ├── test-lem-combine.R │ ├── test-lem-subset.R │ ├── test-more-combine.R │ ├── test-reduced.dim.matrix.R │ ├── test-rowPairs.R │ ├── test-sce-altExp.R │ ├── test-sce-class.R │ ├── test-sce-combine.R │ ├── test-sce-methods.R │ ├── test-sce-reducedDims.R │ ├── test-sce-subset.R │ ├── test-sce-with-lem.R │ └── test-unsplit-altexp.R └── vignettes ├── apply.Rmd ├── devel.Rmd └── intro.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/drisso/SingleCellExperiment/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: 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