Files in babelomics/hipathia
HiPathia: High-throughput Pathway Analysis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/chart.R
R/data.R
R/functions.R
R/load.R
R/load_sif.R
R/main.R
R/save.R
R/stats.R
R/testing.R
R/utils.R
README.md
data/brca.rda
data/brca_data.rda
data/brca_design.rda
data/comp.rda
data/exp_data.rda
data/go_vals.rda
data/path_vals.rda
data/results.rda
inst/CITATION
inst/extdata/SIF_ATT_example/hsa00.att
inst/extdata/SIF_ATT_example/hsa00.sif
inst/extdata/SIF_ATT_example/name.pathways_hsa.txt
inst/extdata/pathway-viewer/conf/config.js
inst/extdata/pathway-viewer/conf/nv-config.js
inst/extdata/pathway-viewer/conf/theme.html
inst/extdata/pathway-viewer/css/context.css
inst/extdata/pathway-viewer/css/form.css
inst/extdata/pathway-viewer/css/global.css
inst/extdata/pathway-viewer/fontawesome/css/font-awesome.css
inst/extdata/pathway-viewer/fontawesome/css/font-awesome.css.map
inst/extdata/pathway-viewer/fontawesome/css/font-awesome.min.css
inst/extdata/pathway-viewer/fontawesome/fonts/FontAwesome.otf
inst/extdata/pathway-viewer/fontawesome/fonts/fontawesome-webfont.eot
inst/extdata/pathway-viewer/fontawesome/fonts/fontawesome-webfont.svg
inst/extdata/pathway-viewer/fontawesome/fonts/fontawesome-webfont.ttf
inst/extdata/pathway-viewer/fontawesome/fonts/fontawesome-webfont.woff
inst/extdata/pathway-viewer/fontawesome/fonts/fontawesome-webfont.woff2
inst/extdata/pathway-viewer/fonts/Lato-Light.woff
inst/extdata/pathway-viewer/fonts/Lato-Regular.woff
inst/extdata/pathway-viewer/fonts/Roboto-Light.woff
inst/extdata/pathway-viewer/fonts/Roboto.woff
inst/extdata/pathway-viewer/fonts/fonts.css
inst/extdata/pathway-viewer/fonts/oxygen.woff
inst/extdata/pathway-viewer/fonts/ubuntu.woff
inst/extdata/pathway-viewer/fonts/ubuntumono.woff
inst/extdata/pathway-viewer/index.html
inst/extdata/pathway-viewer/normalize-css/normalize.css
inst/extdata/pathway-viewer/pathway-viewer.html
inst/extdata/pathway-viewer/webcomponentsjs/CustomElements.min.js
inst/extdata/pathway-viewer/webcomponentsjs/HTMLImports.min.js
inst/extdata/pathway-viewer/webcomponentsjs/MutationObserver.min.js
inst/extdata/pathway-viewer/webcomponentsjs/ShadowDOM.min.js
inst/extdata/pathway-viewer/webcomponentsjs/webcomponents-lite.min.js
inst/extdata/pathway-viewer/webcomponentsjs/webcomponents.min.js
inst/extdata/report-files/favicon_grisclaro.png
inst/extdata/report-files/favicon_grisclaro_puntas.png
inst/extdata/report-files/index_template.html
inst/extdata/report-files/report_legend.png
inst/extdata/report-files/report_logo.png
inst/extdata/report-files/report_title.png
man/annotate_paths.Rd
man/brca.Rd
man/brca_data.Rd
man/brca_design.Rd
man/comp.Rd
man/create_report.Rd
man/do_pca.Rd
man/do_wilcoxon.Rd
man/exp_data.Rd
man/get_go_names.Rd
man/get_highest_sig_ancestor.Rd
man/get_node_names.Rd
man/get_nodes_data.Rd
man/get_path_names.Rd
man/get_paths_data.Rd
man/get_pathway_functions.Rd
man/get_pathways_annotations.Rd
man/get_pathways_list.Rd
man/get_pathways_summary.Rd
man/go_vals.Rd
man/heatmap_plot.Rd
man/hhead.Rd
man/hipathia.Rd
man/igraphs_upgrade.Rd
man/is_accepted_species.Rd
man/load_annofuns.Rd
man/load_annots.Rd
man/load_entrez_hgnc.Rd
man/load_gobp_frame.Rd
man/load_gobp_net.Rd
man/load_mgi.Rd
man/load_pathways.Rd
man/load_pseudo_mgi.Rd
man/load_xref.Rd
man/mgi_from_sif.Rd
man/multiple_pca_plot.Rd
man/node_color.Rd
man/node_color_per_de.Rd
man/normalize_data.Rd
man/normalize_paths.Rd
man/path_vals.Rd
man/paths_to_go_ancestor.Rd
man/pathway_comparison_plot.Rd
man/pca_plot.Rd
man/quantify_terms.Rd
man/results.Rd
man/save_results.Rd
man/top_pathways.Rd
man/translate_data.Rd
man/translate_matrix.Rd
man/visualize_report.Rd
tests/testthat.R
tests/testthat/test-color-node.R
tests/testthat/test-create-report.R
tests/testthat/test-hhead.R
tests/testthat/test-hipathia.R
tests/testthat/test-load-pathways.R
tests/testthat/test-normalization.R
tests/testthat/test-normalize-paths.R
tests/testthat/test-path-annots.R
tests/testthat/test-path-list.R
tests/testthat/test-path-names.R
tests/testthat/test-path-summary.R
tests/testthat/test-quantify.R
tests/testthat/test-translate-matrix.R
tests/testthat/test-wilcoxon.R
vignettes/hipathia-vignette.Rmd
vignettes/pics/ERBB_decomposed_mini.png
vignettes/pics/ERBB_eff_mini.png
vignettes/pics/hipathia_report_1.png
vignettes/pics/package_guide.png
