├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── GEDI.Rproj ├── LICENSE.md ├── NAMESPACE ├── R ├── RcppExports.R └── scIntegration.v113.allow_fixed_B.R ├── README.md ├── man ├── colData.gedi.Rd ├── dispersion.gedi.Rd ├── getA.gedi.Rd ├── getADB.gedi.Rd ├── getActivityGradients.gedi.Rd ├── getDB.gedi.Rd ├── getDiffExp.gedi.Rd ├── getDiffO.gedi.Rd ├── getDiffQ.gedi.Rd ├── getY.gedi.Rd ├── getY.var.gedi.Rd ├── getZDB.gedi.Rd ├── plot_dispersion.Rd ├── plot_embedding.Rd ├── plot_vectorField.Rd ├── svd.activityGradient.gedi.Rd ├── svd.gedi.Rd ├── svd.joint_vectorField_gradient.gedi.Rd └── svd.vectorField.gedi.Rd ├── src ├── .gitignore ├── Eigen.v9.cpp └── RcppExports.cpp └── vignettes ├── .gitignore ├── GEDI_quick.Rmd ├── GEDI_quick.html ├── GEDI_sample_PBMC.Rmd ├── GEDI_sample_PBMC.html ├── GEDI_splicing.Rmd ├── GEDI_splicing.html ├── GEDI_tf_analysis_PBMC.Rmd └── GEDI_tf_analysis_PBMC.html /.Rbuildignore: -------------------------------------------------------------------------------- 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