├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── submit-a-classifier.md └── workflows │ └── check-standard.yaml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── cell_rules.R ├── classify_cells.R ├── data.R ├── garnett.R ├── garnett_classifier.R ├── gene_rule.R ├── get_training_sample.R ├── methods-cell_rules.R ├── methods-garnett_classifier.R ├── parser.R ├── train_cell_classifier.R └── utils.R ├── README.md ├── code-of-conduct.md ├── data ├── test_cds.rda └── test_classifier.rda ├── garnett.Rproj ├── inst ├── CITATION └── extdata │ ├── exprs_sparse.mtx │ ├── fdata.txt │ ├── pbmc_bad_markers.txt │ ├── pbmc_test.txt │ └── pdata.txt ├── man ├── Parser.Rd ├── cell_rules.Rd ├── check_markers.Rd ├── classify_cells.Rd ├── garnett-package.Rd ├── garnett_classifier.Rd ├── gene_rule-class.Rd ├── get_classifier_references.Rd ├── get_feature_genes.Rd ├── plot_markers.Rd ├── test_cds.Rd ├── test_classifier.Rd └── train_cell_classifier.Rd ├── tests ├── bad_parse1.txt ├── bad_parse2.txt ├── ensembl_test.txt ├── figs │ ├── deps.txt │ └── test-utils-r │ │ ├── basic-marker-plot-change-amb.svg │ │ └── basic-marker-plot.svg ├── good_parse.txt ├── logic_test.txt ├── pbmc_1mark.txt ├── pbmc_get_training.txt ├── pbmc_get_training_bad.txt ├── pbmc_get_training_bad2.txt ├── pbmc_test.txt ├── pbmc_test_dos.txt ├── testthat.R └── testthat │ ├── _snaps │ └── utils │ │ ├── basic-marker-plot-change-amb.svg │ │ └── basic-marker-plot.svg │ ├── test-classify_cells.R │ ├── test-get_training_sample.R │ ├── test-overall.R │ ├── test-parser.R │ ├── test-train_cell_classifier.R │ └── test-utils.R └── vignettes ├── .gitignore └── website-vignette.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cole-trapnell-lab/garnett/HEAD/.Rbuildignore -------------------------------------------------------------------------------- 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