├── .Rbuildignore ├── .github └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── CRAN-RELEASE ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── data.R ├── presto-package.R ├── pseudobulk.R ├── utils.R └── wilcoxauc.R ├── README.md ├── cran-comments.md ├── data ├── exprs.rda ├── object_sce.rda ├── object_seurat.rda └── y.rda ├── docs ├── .nojekyll ├── 404.html ├── articles │ ├── getting-started.html │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── collapse_counts.html │ ├── compute_hash.html │ ├── exprs.html │ ├── index.html │ ├── nnzeroGroups.html │ ├── object_sce.html │ ├── object_seurat.html │ ├── pipe.html │ ├── presto.html │ ├── pseudobulk_deseq2.html │ ├── pseudobulk_one_vs_all.html │ ├── pseudobulk_pairwise.html │ ├── pseudobulk_within.html │ ├── rank_matrix.html │ ├── sumGroups.html │ ├── summarize_dge_pairs.html │ ├── top_markers.html │ ├── top_markers_dds.html │ ├── wilcoxauc.html │ └── y.html └── sitemap.xml ├── man ├── collapse_counts.Rd ├── compute_hash.Rd ├── exprs.Rd ├── nnzeroGroups.Rd ├── object_sce.Rd ├── object_seurat.Rd ├── pipe.Rd ├── presto.Rd ├── pseudobulk_deseq2.Rd ├── pseudobulk_one_vs_all.Rd ├── pseudobulk_pairwise.Rd ├── pseudobulk_within.Rd ├── rank_matrix.Rd ├── sumGroups.Rd ├── summarize_dge_pairs.Rd ├── top_markers.Rd ├── top_markers_dds.Rd ├── wilcoxauc.Rd └── y.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp └── fast_wilcox.cpp ├── tests ├── testthat.R └── testthat │ ├── test_correctness.R │ └── test_datatypes.R └── vignettes ├── getting-started.Rmd └── pseudobulk.ipynb /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/immunogenomics/presto/HEAD/.Rbuildignore 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