├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── 1_prepareData.R ├── 2_transformData.R ├── 3_generateClusters.R ├── calcCounts.R ├── calcMedians.R ├── calcMediansByClusterMarker.R ├── calcMediansBySampleMarker.R ├── createContrast.R ├── createDesignMatrix.R ├── createFormula.R ├── diffcyt_wrapper.R ├── plotHeatmap.R ├── testDA_GLMM.R ├── testDA_edgeR.R ├── testDA_voom.R ├── testDS_LMM.R ├── testDS_limma.R ├── topClusters.R └── topTable.R ├── README.md ├── inst ├── CITATION └── NEWS ├── man ├── calcCounts.Rd ├── calcMedians.Rd ├── calcMediansByClusterMarker.Rd ├── calcMediansBySampleMarker.Rd ├── createContrast.Rd ├── createDesignMatrix.Rd ├── createFormula.Rd ├── diffcyt.Rd ├── generateClusters.Rd ├── plotHeatmap.Rd ├── prepareData.Rd ├── testDA_GLMM.Rd ├── testDA_edgeR.Rd ├── testDA_voom.Rd ├── testDS_LMM.Rd ├── testDS_limma.Rd ├── topClusters.Rd ├── topTable.Rd └── transformData.Rd ├── 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