├── .Rbuildignore ├── .github └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── aggregateData.R ├── bbHW.R ├── calcExprFreqs.R ├── data.R ├── mmDS.R ├── pbDS.R ├── pbFlatten.R ├── pbHeatmap.R ├── pbMDS.R ├── prepSCE.R ├── prepSim.R ├── resDS.R ├── simData.R ├── stagewiseDD.R ├── utils-mmDS.R ├── utils-pbDS.R ├── utils-simData.R ├── utils.R └── validity-checks.R ├── README.md ├── data └── example_sce.rda ├── inst ├── CITATION └── extdata │ ├── 1a.png │ ├── 1b.png │ ├── 1d.png │ ├── bbhw.png │ ├── muscat.png │ └── refs.bib ├── man ├── aggregateData.Rd ├── bbhw.Rd ├── calcExprFreqs.Rd ├── data.Rd ├── gBH.Rd ├── mmDS.Rd ├── pbDS.Rd ├── pbFlatten.Rd ├── pbHeatmap.Rd ├── pbMDS.Rd ├── prepSCE.Rd ├── prepSim.Rd ├── resDS.Rd ├── simData.Rd └── stagewise_DS_DD.Rd ├── tests ├── testthat.R └── testthat │ ├── test-aggregateData.R │ ├── test-calcExprFreqs.R │ ├── test-mmDS.R │ ├── test-pbDS.R │ ├── test-pbHeatmap.R │ ├── test-pbMDS.R │ ├── 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