├── .Rbuildignore ├── .github └── workflows │ └── rhub.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── data.R ├── denoise.R ├── differential_expression.R ├── fit.R ├── generate.R ├── plotting.R ├── umify.R ├── utils.R └── vst.R ├── README.md ├── cran-comments.md ├── data ├── pbmc.rda └── umify_data.rda ├── inst └── CITATION ├── man ├── compare_expression.Rd ├── correct.Rd ├── correct_counts.Rd ├── diff_mean_test.Rd ├── diff_mean_test_conserved.Rd ├── generate.Rd ├── get_model_var.Rd ├── get_nz_median2.Rd ├── get_residual_var.Rd ├── get_residuals.Rd ├── is_outlier.Rd ├── make.sparse.Rd ├── pbmc.Rd ├── plot_model.Rd ├── plot_model_pars.Rd ├── robust_scale.Rd ├── robust_scale_binned.Rd ├── row_gmean.Rd ├── row_var.Rd ├── smooth_via_pca.Rd ├── umify.Rd ├── umify_data.Rd └── vst.Rd ├── revdep ├── .gitignore ├── README.md ├── cran.md ├── email.yml ├── failures.md └── problems.md ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp └── utils.cpp ├── supplement ├── batch_correction.Rmd ├── correcting.Rmd ├── differential_expression.Rmd ├── method_comparison.Rmd ├── np_diff_mean_test.Rmd ├── render_all.R ├── seurat.Rmd ├── smartseq2.Rmd ├── theta_regularization.Rmd ├── umify_apply.Rmd ├── umify_learn.Rmd └── variance_stabilizing_transformation.Rmd └── tests ├── testthat.R └── testthat ├── test_denoising.R ├── test_differential_expression.R ├── test_generate.R ├── test_utils.R └── test_vst.R /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/satijalab/sctransform/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/workflows/rhub.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/satijalab/sctransform/HEAD/.github/workflows/rhub.yaml -------------------------------------------------------------------------------- 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