├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── MUDAN.Rproj ├── NAMESPACE ├── R ├── data.R ├── mudan.R └── mudan_object.R ├── README.md ├── data ├── pbmcA.rda ├── pbmcB.rda ├── pbmcC.rda ├── referenceAnnot.rda └── referenceCounts.rda ├── docs ├── Gemfile ├── Gemfile.lock ├── _config.yml ├── _layouts │ └── default.html ├── _sass │ ├── fonts.scss │ ├── jekyll-theme-minimal.scss │ └── rouge-github.scss ├── assets │ ├── css │ │ └── style.scss │ ├── fonts │ │ ├── Noto-Sans-700 │ │ │ ├── Noto-Sans-700.eot │ │ │ ├── Noto-Sans-700.svg │ │ │ ├── Noto-Sans-700.ttf │ │ │ ├── Noto-Sans-700.woff │ │ │ └── Noto-Sans-700.woff2 │ │ ├── Noto-Sans-700italic │ │ │ ├── Noto-Sans-700italic.eot │ │ │ ├── Noto-Sans-700italic.svg │ │ │ ├── Noto-Sans-700italic.ttf │ │ │ ├── Noto-Sans-700italic.woff │ │ │ └── Noto-Sans-700italic.woff2 │ │ ├── Noto-Sans-italic │ │ │ ├── Noto-Sans-italic.eot │ │ │ ├── Noto-Sans-italic.svg │ │ │ ├── Noto-Sans-italic.ttf │ │ │ ├── Noto-Sans-italic.woff │ │ │ └── Noto-Sans-italic.woff2 │ │ └── Noto-Sans-regular │ │ │ ├── Noto-Sans-regular.eot │ │ │ ├── Noto-Sans-regular.svg │ │ │ ├── Noto-Sans-regular.ttf │ │ │ ├── Noto-Sans-regular.woff │ │ │ └── Noto-Sans-regular.woff2 │ ├── img │ │ ├── batch.png │ │ ├── diffexp.png │ │ ├── logo.png │ │ ├── stability.png │ │ └── visualization.png │ └── js │ │ └── scale.fix.js ├── favicon.ico └── index.md ├── man ├── Mudan.Rd ├── cleanCounts.Rd ├── clusterBasedBatchCorrect.Rd ├── fastPca.Rd ├── getApproxComMembership.Rd ├── getComMembership.Rd ├── getConfidentPreds.Rd ├── getDifferentialGenes.Rd ├── getPcs.Rd ├── getStableClusters.Rd ├── getVariableGenes.Rd ├── mergePredsList.Rd ├── modelLda.Rd ├── normalizeCounts.Rd ├── normalizeVariance.Rd ├── pbmcA.Rd ├── pbmcB.Rd ├── pbmcC.Rd ├── plotEmbedding.Rd ├── predictLds.Rd ├── referenceAnnot.Rd ├── referenceCounts.Rd └── tsneLda.Rd └── vignette ├── demo.Rmd ├── demo.pdf ├── pbmcs.Rmd ├── pbmcs.pdf ├── sim.Rmd ├── sim.pdf ├── utility.Rmd └── utility.pdf /.gitignore: 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