├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── RcppExports.R ├── datasetLiverBrainLung.R ├── dsa.R ├── estimateNoise.R ├── geneCollapse.R ├── generateData.R ├── hinge.R ├── hysime.R ├── linseedObject.R ├── plotProportions.R ├── preprocess.R ├── projectiveProjection.R ├── proportionsLiverBrainLung.R ├── sisal.R ├── softNeg.R ├── utils.R └── vca.R ├── Readme.md ├── Readme_files └── figure-markdown_github │ ├── deconvolution-1.png │ ├── networks-1.png │ ├── networks-2.png │ ├── proportions-1.png │ ├── rtsne-1.png │ └── visi-1.png ├── data ├── datasetLiverBrainLung.RData └── proportionsLiverBrainLung.RData ├── man ├── LinseedObject.Rd ├── collapseGenes.Rd ├── datasetLiverBrainLung.Rd ├── dotPlotPropotions.Rd ├── estimateAdditiveNoise.Rd ├── estimateNoise.Rd ├── fastDSA.Rd ├── generateMixedData.Rd ├── getProjectiveProjection.Rd ├── guessOrder.Rd ├── hinge.Rd ├── hysime.Rd ├── is_logscale.Rd ├── linearizeDataset.Rd ├── logDataset.Rd ├── plotProportions.Rd ├── preprocessDataset.Rd ├── preprocessGSE.Rd ├── projectiveProjection.Rd ├── proportionsLiverBrainLung.Rd ├── pureDsa.Rd ├── runDSA.Rd ├── sampleFromSimplexUniformly.Rd ├── sisal.Rd ├── softNeg.Rd └── vca.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── fcnnls.cpp ├── fcnnls.h └── pairwiseR2.cpp └── vignettes └── linseedTutorial.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctlab/LinSeed/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ctlab/LinSeed/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 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