├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── CRAN-SUBMISSION ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── RcppExports.R ├── RunHarmony.R ├── data.R ├── harmony-package.r ├── harmony_option.R ├── ui.R └── utils.R ├── README.md ├── appveyor.yml ├── cran-comments.md ├── data ├── cell_lines.rda ├── cell_lines_small.RData └── pbmc_stim.RData ├── doc ├── Seurat.R ├── Seurat.Rmd ├── Seurat.html ├── detailedWalkthrough.R ├── detailedWalkthrough.Rmd ├── detailedWalkthrough.html ├── parameters.R ├── parameters.Rmd ├── parameters.html ├── quickstart.R ├── quickstart.Rmd └── quickstart.html ├── man ├── HarmonyMatrix.Rd ├── RunHarmony.Rd ├── RunHarmony.Seurat.Rd ├── RunHarmony.SingleCellExperiment.Rd ├── RunHarmony.default.Rd ├── cell_lines.Rd ├── cell_lines_small.Rd ├── figures │ └── logo.png ├── harmony.Rd ├── harmony_options.Rd ├── moe_ridge_get_betas.Rd ├── pbmc.ctrl.Rd ├── pbmc.stim.Rd └── pipe.Rd ├── src ├── .gitignore ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── harmony.cpp ├── harmony.h ├── harmony_types.h ├── types.h ├── utils.cpp └── utils.h ├── tests ├── testthat.R └── testthat │ └── test_integration.R └── vignettes ├── .gitignore ├── Seurat.Rmd ├── detailedWalkthrough.Rmd ├── main.jpg └── quickstart.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/.travis.yml -------------------------------------------------------------------------------- /CRAN-SUBMISSION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/CRAN-SUBMISSION -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/NEWS -------------------------------------------------------------------------------- /R/RcppExports.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/R/RcppExports.R -------------------------------------------------------------------------------- /R/RunHarmony.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/R/RunHarmony.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/R/data.R -------------------------------------------------------------------------------- /R/harmony-package.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/R/harmony-package.r -------------------------------------------------------------------------------- /R/harmony_option.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/R/harmony_option.R -------------------------------------------------------------------------------- /R/ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/R/ui.R -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/R/utils.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/README.md -------------------------------------------------------------------------------- /appveyor.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/appveyor.yml -------------------------------------------------------------------------------- /cran-comments.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/cran-comments.md -------------------------------------------------------------------------------- /data/cell_lines.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/data/cell_lines.rda -------------------------------------------------------------------------------- /data/cell_lines_small.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/data/cell_lines_small.RData -------------------------------------------------------------------------------- /data/pbmc_stim.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/data/pbmc_stim.RData -------------------------------------------------------------------------------- /doc/Seurat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/Seurat.R -------------------------------------------------------------------------------- /doc/Seurat.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/Seurat.Rmd -------------------------------------------------------------------------------- /doc/Seurat.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/Seurat.html -------------------------------------------------------------------------------- /doc/detailedWalkthrough.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/detailedWalkthrough.R -------------------------------------------------------------------------------- /doc/detailedWalkthrough.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/detailedWalkthrough.Rmd -------------------------------------------------------------------------------- /doc/detailedWalkthrough.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/detailedWalkthrough.html -------------------------------------------------------------------------------- /doc/parameters.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/parameters.R -------------------------------------------------------------------------------- /doc/parameters.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/parameters.Rmd -------------------------------------------------------------------------------- /doc/parameters.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/parameters.html -------------------------------------------------------------------------------- /doc/quickstart.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/quickstart.R -------------------------------------------------------------------------------- /doc/quickstart.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/quickstart.Rmd -------------------------------------------------------------------------------- /doc/quickstart.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/doc/quickstart.html -------------------------------------------------------------------------------- /man/HarmonyMatrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/HarmonyMatrix.Rd -------------------------------------------------------------------------------- /man/RunHarmony.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/RunHarmony.Rd -------------------------------------------------------------------------------- /man/RunHarmony.Seurat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/RunHarmony.Seurat.Rd -------------------------------------------------------------------------------- /man/RunHarmony.SingleCellExperiment.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/RunHarmony.SingleCellExperiment.Rd -------------------------------------------------------------------------------- /man/RunHarmony.default.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/RunHarmony.default.Rd -------------------------------------------------------------------------------- /man/cell_lines.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/cell_lines.Rd -------------------------------------------------------------------------------- /man/cell_lines_small.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/cell_lines_small.Rd -------------------------------------------------------------------------------- /man/figures/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/figures/logo.png -------------------------------------------------------------------------------- /man/harmony.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/harmony.Rd -------------------------------------------------------------------------------- /man/harmony_options.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/harmony_options.Rd -------------------------------------------------------------------------------- /man/moe_ridge_get_betas.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/moe_ridge_get_betas.Rd -------------------------------------------------------------------------------- /man/pbmc.ctrl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/pbmc.ctrl.Rd -------------------------------------------------------------------------------- /man/pbmc.stim.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/pbmc.stim.Rd -------------------------------------------------------------------------------- /man/pipe.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/man/pipe.Rd -------------------------------------------------------------------------------- /src/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/.gitignore -------------------------------------------------------------------------------- /src/Makevars: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/Makevars -------------------------------------------------------------------------------- /src/Makevars.win: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/Makevars.win -------------------------------------------------------------------------------- /src/RcppExports.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/RcppExports.cpp -------------------------------------------------------------------------------- /src/harmony.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/harmony.cpp -------------------------------------------------------------------------------- /src/harmony.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/harmony.h -------------------------------------------------------------------------------- /src/harmony_types.h: -------------------------------------------------------------------------------- 1 | #include "types.h" 2 | 3 | -------------------------------------------------------------------------------- /src/types.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/types.h -------------------------------------------------------------------------------- /src/utils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/utils.cpp -------------------------------------------------------------------------------- /src/utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/src/utils.h -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test_integration.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/tests/testthat/test_integration.R -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /vignettes/Seurat.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/vignettes/Seurat.Rmd -------------------------------------------------------------------------------- /vignettes/detailedWalkthrough.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/vignettes/detailedWalkthrough.Rmd -------------------------------------------------------------------------------- /vignettes/main.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/vignettes/main.jpg -------------------------------------------------------------------------------- /vignettes/quickstart.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/harmony/HEAD/vignettes/quickstart.Rmd --------------------------------------------------------------------------------