├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── analysis.R ├── cytotalk.R ├── data.R ├── fileio.R ├── graphing.R ├── integrated.R ├── matrix.R ├── mutinfo.R ├── parallel.R ├── pcst.R ├── pem.R └── utils.R ├── README.Rmd ├── README.md ├── data ├── lrp_human.rda ├── lrp_mouse.rda ├── pcg_human.rda ├── pcg_mouse.rda ├── protetta.rda ├── result_cyto.rda ├── scrna_cpdb.rda └── scrna_cyto.rda ├── docs ├── cytoscape_network.svg ├── cytotalk_diagram.png └── pathway.svg ├── man ├── analyze_pathway.Rd ├── check_count_data.Rd ├── doc_graphing.Rd ├── doc_integrated.Rd ├── doc_mutinfo.Rd ├── doc_parallel.Rd ├── doc_pcst.Rd ├── doc_pem.Rd ├── extract_group.Rd ├── from_single_cell_experiment.Rd ├── group_meta.Rd ├── lrp_human.Rd ├── lrp_mouse.Rd ├── match_lr_pairs.Rd ├── normalize_sparse.Rd ├── pcg_human.Rd ├── pcg_mouse.Rd ├── protetta.Rd ├── read_matrix_folder.Rd ├── read_matrix_with_meta.Rd ├── result_cyto.Rd ├── run_cytotalk.Rd ├── scrna_cpdb.Rd ├── scrna_cyto.Rd ├── subset_non_zero.Rd ├── subset_rownames.Rd └── ungroup_meta.Rd ├── tests ├── testthat.R └── testthat │ └── test_matrix.R └── vignettes ├── .gitignore └── cytotalk_guide.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tanlabcode/CytoTalk/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | inst/doc 4 | test_script.R* 5 | /doc/ 6 | /Meta/ 7 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tanlabcode/CytoTalk/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: 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