Files in tbilab/meToolkit

Build and Customize Phewas Multimorbidity Explorer Apps.

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

R/app_build_me_dashboard.R R/app_build_me_w_loader.R R/helpers_calc_pattern_risk_ratio.R R/helpers_data_validation_functions.R R/helpers_for_main_dashboard.R R/helpers_normalize_phecodes.R R/helpers_reconcile_data.R R/helpers_url_state_managers.R R/mod_data_loader.R R/mod_help_modal.R R/mod_info_panel.R R/mod_main_dashboard.R R/mod_manhattan_and_table.R R/mod_network_plot.R R/mod_upset.R R/sim_individual_data.R R/sim_phewas_results.R

R/sysdata.rda

R/utils-pipe.R README.md

_pkgdown.yml

data-raw/phecode_definitions1.2.csv

data-raw/phecode_descriptions.R data-raw/snp_annotations.R

data/fake_info_data.rds

data/fake_info_options.rds

data/fake_network_data.rds

data/fake_network_options.rds

data/fake_phewas_results.rda

data/fake_upset_main.rds

data/fake_upset_options.rds

data/full_exome_annotations.csv

data/manhattan_test_data.rds

data/manhattan_test_options.rds

data/phecode_descriptions.rda

data/snp_annotations.rda

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/data_loading_screen.png

docs/articles/index.html

docs/articles/info_panel.png

docs/articles/loading_page.png

docs/articles/main_dashboard.png

docs/articles/manhattan_plot.png

docs/articles/meToolkit.html

docs/articles/network_help_page.png

docs/articles/network_plot.png

docs/articles/phewas_help_page.png

docs/articles/subject_download_btn.png

docs/articles/upset_help_page.png

docs/articles/upset_plot.png

docs/authors.html

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/buildColorPalette.html

docs/reference/build_color_palette.html

docs/reference/build_me_app.html

docs/reference/build_me_dashboard.html

docs/reference/build_me_w_loader.html

docs/reference/calcRrCi.html

docs/reference/calc_pattern_risk_ratio.html

docs/reference/checkGenomeFile.html

docs/reference/checkPhenomeFile.html

docs/reference/checkPhewasFile.html

docs/reference/check_genome_file.html

docs/reference/check_phenome_file.html

docs/reference/check_phewas_file.html

docs/reference/codeFilter.html

docs/reference/data_loader.html

docs/reference/data_loader_UI.html

docs/reference/deleteCodes.html

docs/reference/detect_id_column.html

docs/reference/embed_snp_codes_in_url.html

docs/reference/extract_snp_codes_from_url.html

docs/reference/extract_snp_codes_from_url_string.html

docs/reference/gather_snp_annotations.html

docs/reference/hello.html

docs/reference/help_modal.html

docs/reference/help_modal_UI.html

docs/reference/index.html

docs/reference/info_panel.html

docs/reference/info_panel_UI.html

docs/reference/invertCodes.html

docs/reference/isolateCodes.html

docs/reference/main_dashboard.html

docs/reference/main_dashboard_UI.html

docs/reference/makeDescriptionPalette.html

docs/reference/makeNetworkData.html

docs/reference/manhattan_plot_and_table.html

docs/reference/manhattan_plot_and_table_UI.html

docs/reference/mergePhenomeGenome.html

docs/reference/network_plot.html

docs/reference/network_plot_UI.html

docs/reference/normalizePhecode.html

docs/reference/normalize_phecodes.html

docs/reference/pipe.html

docs/reference/pretty_popup.html

docs/reference/reconcile_data.html

docs/reference/reveal_element.html

docs/reference/run_me.html

docs/reference/setup_network_data.html

docs/reference/simIndividualData.html

docs/reference/simPhewasResults.html

docs/reference/sim_individual_data.html

docs/reference/sim_phewas_results.html

docs/reference/subsetToCodes.html

docs/reference/subset_to_codes.html

docs/reference/upset.html

docs/reference/upset_UI.html

docs/reference/use_pretty_popup.html

docs/reference/use_reveal_element.html

inst/css/common.css

inst/d3/helpers.css

inst/d3/helpers.js

inst/d3/info_panel/info_panel.css

inst/d3/info_panel/info_panel.js

inst/d3/manhattan_plot/clusterize.js

inst/d3/manhattan_plot/manhattan_plot.css

inst/d3/manhattan_plot/manhattan_plot.js

inst/d3/manhattan_plot/phewas_table.js

inst/d3/network_plot/helpers.js

inst/d3/network_plot/index.js

inst/d3/network_plot/network.css

inst/d3/setup_data_for_network_building.R inst/d3/setup_data_for_r2d3_building.R

inst/d3/upset/helpers.js

inst/d3/upset/upset.css

inst/d3/upset/upset.js

inst/data_instructions.md inst/data_loading_app/app.R

inst/data_loading_app/preloaded_data/id_to_code.csv

inst/data_loading_app/preloaded_data/rs123456/id_to_snp.csv

inst/data_loading_app/preloaded_data/rs123456/phewas_results.csv

inst/demo_app/app.R

inst/demo_app/data/id_to_phenome.csv

inst/demo_app/data/id_to_snp.csv

inst/demo_app/data/phewas_results.csv

inst/demo_app/tests/shinytest.R

inst/demo_app/tests/shinytests/custom_test-current/001.json

inst/demo_app/tests/shinytests/custom_test-current/001.png

inst/demo_app/tests/shinytests/mytest-current/001.json

inst/demo_app/tests/shinytests/mytest-current/001.png

inst/demo_app/tests/shinytests/mytest-expected/001.json

inst/demo_app/tests/shinytests/mytest-expected/001.png

inst/demo_app/tests/shinytests/mytest.R

inst/html_templates/data_loading_template.html

inst/html_templates/empty_page.html

inst/html_templates/main_dashboard.html

inst/manhattan_only/app.R

inst/sample_data/id_to_phenome.csv

inst/sample_data/id_to_snp.csv

inst/sample_data/phewas_results.csv

inst/sample_data/rs12345

man/build_me_dashboard.Rd man/build_me_w_loader.Rd man/calc_pattern_risk_ratio.Rd man/check_genome_file.Rd man/check_phenome_file.Rd man/check_phewas_file.Rd man/data_loader.Rd man/data_loader_UI.Rd man/embed_snp_codes_in_url.Rd man/extract_snp_codes_from_url.Rd man/extract_snp_codes_from_url_string.Rd man/help_modal.Rd man/help_modal_UI.Rd man/info_panel.Rd man/info_panel_UI.Rd man/main_dashboard.Rd man/main_dashboard_UI.Rd man/manhattan_plot_and_table.Rd man/manhattan_plot_and_table_UI.Rd man/network_plot.Rd man/network_plot_UI.Rd man/normalize_phecodes.Rd man/pipe.Rd man/reconcile_data.Rd man/setup_network_data.Rd man/sim_individual_data.Rd man/sim_phewas_results.Rd man/subset_to_codes.Rd man/upset.Rd man/upset_UI.Rd

meToolkit.Rproj

tests/setup_shinytests.R tests/shinytests/custom_shinytest_experiment.R tests/testthat.R tests/testthat/test-calc_pattern_risk_ratio.R tests/testthat/test-data_validating.R tests/testthat/test-demo_apps.R tests/testthat/test-normalize_phecode.R tests/testthat/test-reconcile_data.R tests/testthat/test-setup_network_data.R tests/testthat/test-sim_individual_data.R tests/testthat/test-sim_phewas_results.R tests/testthat/test-subset_to_codes.R tools/deploy_docs.R

vignettes/.gitignore

vignettes/_manuscript_appendix.Rmd

vignettes/data_loading_screen.png

vignettes/info_panel.png

vignettes/main_dashboard.png

vignettes/meToolkit.Rmd

vignettes/network_help_page.png

vignettes/phewas_help_page.png

vignettes/subject_download_btn.png

vignettes/upset_help_page.png

tbilab/meToolkit documentation built on June 23, 2020, 9:55 a.m.