├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── PerseusR.Rproj ├── R ├── io.R ├── matrixData.R ├── matrixDataMethods.R └── params.R ├── README.md ├── cran-comments.md ├── inst └── extdata │ ├── matrix1.txt │ ├── matrix2.txt │ ├── matrix3.txt │ ├── matrix4.txt │ └── parameters1.xml ├── man ├── MatrixDataCheck.Rd ├── annotCols-set.Rd ├── annotCols.Rd ├── annotRows-set.Rd ├── annotRows.Rd ├── as.ExpressionSet.matrixData.Rd ├── as.matrixData.ExpressionSet.Rd ├── boolParamValue.Rd ├── create_annotRows.Rd ├── description-set.Rd ├── description.Rd ├── imputeData-set.Rd ├── imputeData.Rd ├── infer_perseus_annotation_types.Rd ├── initialize-matrixData-method.Rd ├── intParamValue.Rd ├── main-set.Rd ├── main.Rd ├── matrixData-class.Rd ├── matrixData-methods.Rd ├── matrixData.Rd ├── multiChoiceParamValue.Rd ├── names.matrixData.Rd ├── parseParameters.Rd ├── qualityData-set.Rd ├── qualityData.Rd ├── read.perseus.Rd ├── singleChoiceParamInd.Rd ├── singleChoiceParamValue.Rd ├── stringParamValue.Rd └── write.perseus.Rd ├── tests ├── testthat.R └── testthat │ ├── testCoercionMethods.R │ ├── testIO.R │ ├── testMatrixData.R │ └── testParameters.R └── vignettes └── Using-Perseus-data-in-R.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cox-labs/PerseusR/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cox-labs/PerseusR/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cox-labs/PerseusR/HEAD/.travis.yml 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