├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── checkArgs.R ├── contrastiveCov.R ├── covMat.R ├── exampleData.R ├── fitCPCA.R ├── fitGrid.R ├── safeColScale.R ├── scPCA.R └── spcaWrapper.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── appveyor.yml ├── codecov.yml ├── data ├── background_df.rda └── toy_df.rda ├── docs ├── articles │ └── scpca_intro_files │ │ ├── figure-html │ │ ├── PCA_sim-1.png │ │ ├── cPCA_sim-1.png │ │ ├── microbenchmark_comparison-1.png │ │ ├── plot_cv_cPCA_scPCA-1.png │ │ ├── plot_red_dims-1.png │ │ ├── sPCA_sim-1.png │ │ ├── scPCA_sim-1.png │ │ └── scPCA_sim-2.png │ │ └── header-attrs-2.6 │ │ └── header-attrs.js ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── Rplot001.png │ └── figures │ └── README-pressure-1.png ├── inst ├── CITATION └── REFERENCES.bib ├── man ├── background_df.Rd ├── bpContrastiveCov.Rd ├── bpFitCPCA.Rd ├── bpFitGrid.Rd ├── checkArgs.Rd ├── contrastiveCov.Rd ├── covMat.Rd ├── cvSelectParams.Rd ├── figures │ └── README-pressure-1.png ├── fitCPCA.Rd ├── fitGrid.Rd ├── safeColScale.Rd ├── scPCA.Rd ├── selectParams.Rd ├── spcaWrapper.Rd └── toy_df.Rd ├── manuscript ├── paper.bib └── paper.md ├── tests ├── testthat.R └── testthat │ ├── test-checkArgs.R │ ├── test-contrastiveCov.R │ ├── test-covMat.R │ ├── test-fitCPCA.R │ ├── test-fitGrid.R │ ├── test-safeColScale.R │ └── test-scPCA.R └── vignettes └── scpca_intro.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PhilBoileau/scPCA/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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