├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── CEMiTool.Rproj ├── DESCRIPTION ├── NAMESPACE ├── R ├── cemitool.R ├── datasets.R ├── diagnostics.R ├── enrichment.R ├── filter.R ├── interactions.R ├── modules.R ├── report.R ├── utils.R └── visualization.R ├── README.md ├── data ├── cem.rda ├── expr0.rda └── sample_annot.rda ├── docker ├── Dockerfile ├── Dockerfile.build ├── example.md └── install-deps.R ├── exec └── CEMiTool.R ├── inst ├── CITATION ├── diagnostics │ └── diagnostics.Rmd ├── extdata │ ├── interactions.tsv │ └── pathways.gmt └── report │ └── report.Rmd ├── man ├── CEMiTool-class.Rd ├── adj_data.Rd ├── cem.Rd ├── cemitool.Rd ├── diagnostic_report.Rd ├── expr0.Rd ├── expr_data.Rd ├── expr_pct_filter.Rd ├── filter_expr.Rd ├── find_modules.Rd ├── fit_data.Rd ├── generate_report.Rd ├── get_adj.Rd ├── get_beta_data.Rd ├── get_cemitool_r2_beta.Rd ├── get_connectivity.Rd ├── get_hubs.Rd ├── get_merged_mods.Rd ├── get_mods.Rd ├── get_phi.Rd ├── gsea_data.Rd ├── interactions_data.Rd ├── mod_colors.Rd ├── mod_gene_num.Rd ├── mod_gsea.Rd ├── mod_names.Rd ├── mod_ora.Rd ├── mod_summary.Rd ├── module_genes.Rd ├── module_to_gmt.Rd ├── new_cem.Rd ├── nmodules.Rd ├── ora_data.Rd ├── plot_beta_r2.Rd ├── plot_gsea.Rd ├── plot_hist.Rd ├── plot_interactions.Rd ├── plot_mean_k.Rd ├── plot_mean_var.Rd ├── plot_ora.Rd ├── plot_ora_single.Rd ├── plot_profile.Rd ├── plot_qq.Rd ├── plot_sample_tree.Rd ├── read_gmt.Rd ├── sample_annot.Rd ├── sample_annotation.Rd ├── save_plots.Rd ├── select_genes.Rd ├── show-CEMiTool-method.Rd ├── show_plot.Rd ├── vst.Rd └── write_files.Rd ├── tests ├── testthat.R └── testthat │ ├── test-adj_data.R │ ├── test-cemitool.R │ ├── test-diagnostic_plots.R │ ├── test-expr_data.R │ ├── test-filter_select.R │ ├── test-find_modules.R │ ├── test-generate_report.R │ ├── test-get_adj.R │ ├── test-get_hubs.R │ ├── test-interactions_data.R │ ├── test-mod_colors.R │ ├── test-mod_gene_num.R │ ├── test-mod_gsea.R │ ├── test-mod_names.R │ ├── test-mod_ora.R │ ├── test-mod_summary.R │ ├── test-new_cem.R │ ├── test-nmodules.R │ ├── test-plot_beta_r2.R │ ├── test-plot_gsea.R │ ├── test-plot_interactions.R │ ├── test-plot_mean_k.R │ ├── test-plot_ora.R │ ├── test-plot_profile.R │ └── test-sample_annotation.R └── vignettes └── CEMiTool.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/.travis.yml -------------------------------------------------------------------------------- /CEMiTool.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/CEMiTool.Rproj -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/cemitool.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/cemitool.R -------------------------------------------------------------------------------- /R/datasets.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/datasets.R -------------------------------------------------------------------------------- /R/diagnostics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/diagnostics.R -------------------------------------------------------------------------------- /R/enrichment.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/enrichment.R -------------------------------------------------------------------------------- /R/filter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/filter.R -------------------------------------------------------------------------------- /R/interactions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/interactions.R -------------------------------------------------------------------------------- /R/modules.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/modules.R -------------------------------------------------------------------------------- /R/report.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/report.R -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/utils.R -------------------------------------------------------------------------------- /R/visualization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/R/visualization.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/README.md -------------------------------------------------------------------------------- /data/cem.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/data/cem.rda -------------------------------------------------------------------------------- /data/expr0.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/data/expr0.rda -------------------------------------------------------------------------------- /data/sample_annot.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/data/sample_annot.rda -------------------------------------------------------------------------------- /docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/docker/Dockerfile -------------------------------------------------------------------------------- /docker/Dockerfile.build: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/docker/Dockerfile.build -------------------------------------------------------------------------------- /docker/example.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/docker/example.md -------------------------------------------------------------------------------- /docker/install-deps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/docker/install-deps.R -------------------------------------------------------------------------------- /exec/CEMiTool.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/exec/CEMiTool.R -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/inst/CITATION -------------------------------------------------------------------------------- /inst/diagnostics/diagnostics.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/inst/diagnostics/diagnostics.Rmd -------------------------------------------------------------------------------- /inst/extdata/interactions.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/inst/extdata/interactions.tsv -------------------------------------------------------------------------------- /inst/extdata/pathways.gmt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/inst/extdata/pathways.gmt -------------------------------------------------------------------------------- /inst/report/report.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/inst/report/report.Rmd -------------------------------------------------------------------------------- /man/CEMiTool-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/CEMiTool-class.Rd -------------------------------------------------------------------------------- /man/adj_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/adj_data.Rd -------------------------------------------------------------------------------- /man/cem.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/cem.Rd -------------------------------------------------------------------------------- /man/cemitool.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/cemitool.Rd -------------------------------------------------------------------------------- /man/diagnostic_report.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/diagnostic_report.Rd -------------------------------------------------------------------------------- /man/expr0.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/expr0.Rd -------------------------------------------------------------------------------- /man/expr_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/expr_data.Rd -------------------------------------------------------------------------------- /man/expr_pct_filter.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/expr_pct_filter.Rd -------------------------------------------------------------------------------- /man/filter_expr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/filter_expr.Rd -------------------------------------------------------------------------------- /man/find_modules.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/find_modules.Rd -------------------------------------------------------------------------------- /man/fit_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/fit_data.Rd -------------------------------------------------------------------------------- /man/generate_report.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/generate_report.Rd -------------------------------------------------------------------------------- /man/get_adj.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/get_adj.Rd -------------------------------------------------------------------------------- /man/get_beta_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/get_beta_data.Rd -------------------------------------------------------------------------------- /man/get_cemitool_r2_beta.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/get_cemitool_r2_beta.Rd -------------------------------------------------------------------------------- /man/get_connectivity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/get_connectivity.Rd -------------------------------------------------------------------------------- /man/get_hubs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/get_hubs.Rd -------------------------------------------------------------------------------- /man/get_merged_mods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/get_merged_mods.Rd -------------------------------------------------------------------------------- /man/get_mods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/get_mods.Rd -------------------------------------------------------------------------------- /man/get_phi.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/get_phi.Rd -------------------------------------------------------------------------------- /man/gsea_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/gsea_data.Rd -------------------------------------------------------------------------------- /man/interactions_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/interactions_data.Rd -------------------------------------------------------------------------------- /man/mod_colors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/mod_colors.Rd -------------------------------------------------------------------------------- /man/mod_gene_num.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/mod_gene_num.Rd -------------------------------------------------------------------------------- /man/mod_gsea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/mod_gsea.Rd -------------------------------------------------------------------------------- /man/mod_names.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/mod_names.Rd -------------------------------------------------------------------------------- /man/mod_ora.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/mod_ora.Rd -------------------------------------------------------------------------------- /man/mod_summary.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/mod_summary.Rd -------------------------------------------------------------------------------- /man/module_genes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/module_genes.Rd -------------------------------------------------------------------------------- /man/module_to_gmt.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/module_to_gmt.Rd -------------------------------------------------------------------------------- /man/new_cem.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/new_cem.Rd -------------------------------------------------------------------------------- /man/nmodules.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/nmodules.Rd -------------------------------------------------------------------------------- /man/ora_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/ora_data.Rd -------------------------------------------------------------------------------- /man/plot_beta_r2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_beta_r2.Rd -------------------------------------------------------------------------------- /man/plot_gsea.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_gsea.Rd -------------------------------------------------------------------------------- /man/plot_hist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_hist.Rd -------------------------------------------------------------------------------- /man/plot_interactions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_interactions.Rd -------------------------------------------------------------------------------- /man/plot_mean_k.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_mean_k.Rd -------------------------------------------------------------------------------- /man/plot_mean_var.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_mean_var.Rd -------------------------------------------------------------------------------- /man/plot_ora.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_ora.Rd -------------------------------------------------------------------------------- /man/plot_ora_single.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_ora_single.Rd -------------------------------------------------------------------------------- /man/plot_profile.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_profile.Rd -------------------------------------------------------------------------------- /man/plot_qq.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_qq.Rd -------------------------------------------------------------------------------- /man/plot_sample_tree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/plot_sample_tree.Rd -------------------------------------------------------------------------------- /man/read_gmt.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/read_gmt.Rd -------------------------------------------------------------------------------- /man/sample_annot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/sample_annot.Rd -------------------------------------------------------------------------------- /man/sample_annotation.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/sample_annotation.Rd -------------------------------------------------------------------------------- /man/save_plots.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/save_plots.Rd -------------------------------------------------------------------------------- /man/select_genes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/select_genes.Rd -------------------------------------------------------------------------------- /man/show-CEMiTool-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/show-CEMiTool-method.Rd -------------------------------------------------------------------------------- /man/show_plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/show_plot.Rd -------------------------------------------------------------------------------- /man/vst.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/vst.Rd -------------------------------------------------------------------------------- /man/write_files.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/man/write_files.Rd -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test-adj_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-adj_data.R -------------------------------------------------------------------------------- /tests/testthat/test-cemitool.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-cemitool.R -------------------------------------------------------------------------------- /tests/testthat/test-diagnostic_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-diagnostic_plots.R -------------------------------------------------------------------------------- /tests/testthat/test-expr_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-expr_data.R -------------------------------------------------------------------------------- /tests/testthat/test-filter_select.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-filter_select.R -------------------------------------------------------------------------------- /tests/testthat/test-find_modules.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-find_modules.R -------------------------------------------------------------------------------- /tests/testthat/test-generate_report.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-generate_report.R -------------------------------------------------------------------------------- /tests/testthat/test-get_adj.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-get_adj.R -------------------------------------------------------------------------------- /tests/testthat/test-get_hubs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-get_hubs.R -------------------------------------------------------------------------------- /tests/testthat/test-interactions_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-interactions_data.R -------------------------------------------------------------------------------- /tests/testthat/test-mod_colors.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-mod_colors.R -------------------------------------------------------------------------------- /tests/testthat/test-mod_gene_num.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-mod_gene_num.R -------------------------------------------------------------------------------- /tests/testthat/test-mod_gsea.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-mod_gsea.R -------------------------------------------------------------------------------- /tests/testthat/test-mod_names.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-mod_names.R -------------------------------------------------------------------------------- /tests/testthat/test-mod_ora.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-mod_ora.R -------------------------------------------------------------------------------- /tests/testthat/test-mod_summary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-mod_summary.R -------------------------------------------------------------------------------- /tests/testthat/test-new_cem.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-new_cem.R -------------------------------------------------------------------------------- /tests/testthat/test-nmodules.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-nmodules.R -------------------------------------------------------------------------------- /tests/testthat/test-plot_beta_r2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-plot_beta_r2.R -------------------------------------------------------------------------------- /tests/testthat/test-plot_gsea.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-plot_gsea.R -------------------------------------------------------------------------------- /tests/testthat/test-plot_interactions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-plot_interactions.R -------------------------------------------------------------------------------- /tests/testthat/test-plot_mean_k.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-plot_mean_k.R -------------------------------------------------------------------------------- /tests/testthat/test-plot_ora.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-plot_ora.R -------------------------------------------------------------------------------- /tests/testthat/test-plot_profile.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-plot_profile.R -------------------------------------------------------------------------------- /tests/testthat/test-sample_annotation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/tests/testthat/test-sample_annotation.R -------------------------------------------------------------------------------- /vignettes/CEMiTool.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csbl-usp/CEMiTool/HEAD/vignettes/CEMiTool.Rmd --------------------------------------------------------------------------------