Files in vjcitn/YESCDS
Cancer data science activities for CZI YES for CURE collaboration
.github/workflows/build_rstudio.yaml
.github/workflows/generate_ipynb.yaml
.github/workflows/jupyter_build.yaml
Cancer_Data_Science_Topics.png
DESCRIPTION
NAMESPACE
R/CIplots.R
R/build_deck.R
R/build_surv.R
R/cache_hcc.R
R/cancer_map_world.R
R/data.R
R/map_app.R
R/mass_map.R
R/ordered_seg_cal.R
R/plot_seer_trend.R
R/poker.R
R/stapp.R
R/survcode.R
R/tabs.R
R/viz.R
README.md
SEER_2018.csv
SEER_2018.rds
_pkgdown.yml
data/SEER_2018.rda
data/brcamutSE.rda
data/canada_crude.rda
data/datalist
data/metabric.rda
data/prostate_met_adeno.rda
data/statcrunch_msa.rda
data/us_county_geo.rda
data/vjc_cancer_net.rda
data/woncan.rda
data/woncan_meta.rda
data/world_cancer_2020_all.rda
data/world_geo_sf.rda
docs/.DS_Store
docs/._.DS_Store
docs/._index.html
docs/404.html
docs/articles/A0_intro_notebook.html
docs/articles/A0_intro_notebook_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/A1_cancer_table.html
docs/articles/A1_cancer_table_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/A1_cancer_table_files/crosstalk-1.2.1/css/crosstalk.min.css
docs/articles/A1_cancer_table_files/crosstalk-1.2.1/js/crosstalk.js
docs/articles/A1_cancer_table_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/articles/A1_cancer_table_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/articles/A1_cancer_table_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/articles/A1_cancer_table_files/crosstalk-1.2.1/scss/crosstalk.scss
docs/articles/A1_cancer_table_files/datatables-binding-0.33/datatables.js
docs/articles/A1_cancer_table_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/A1_cancer_table_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
docs/articles/A1_cancer_table_files/dt-core-1.13.6/css/jquery.dataTables.min.css
docs/articles/A1_cancer_table_files/dt-core-1.13.6/js/jquery.dataTables.min.js
docs/articles/A1_cancer_table_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/A1_cancer_table_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/A2_rates.html
docs/articles/A2_rates_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/A3_monitoring.html
docs/articles/A3_monitoring_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/A4_interactive_tables.html
docs/articles/A4_interactive_tables_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/A4_interactive_tables_files/crosstalk-1.2.1/css/crosstalk.min.css
docs/articles/A4_interactive_tables_files/crosstalk-1.2.1/js/crosstalk.js
docs/articles/A4_interactive_tables_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/articles/A4_interactive_tables_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/articles/A4_interactive_tables_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/articles/A4_interactive_tables_files/crosstalk-1.2.1/scss/crosstalk.scss
docs/articles/A4_interactive_tables_files/datatables-binding-0.33/datatables.js
docs/articles/A4_interactive_tables_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/A4_interactive_tables_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
docs/articles/A4_interactive_tables_files/dt-core-1.13.6/css/jquery.dataTables.min.css
docs/articles/A4_interactive_tables_files/dt-core-1.13.6/js/jquery.dataTables.min.js
docs/articles/A4_interactive_tables_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/A4_interactive_tables_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/A5_data_graphics.html
docs/articles/A5_data_graphics_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/A5_data_graphics_files/crosstalk-1.2.1/css/crosstalk.min.css
docs/articles/A5_data_graphics_files/crosstalk-1.2.1/js/crosstalk.js
docs/articles/A5_data_graphics_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/articles/A5_data_graphics_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/articles/A5_data_graphics_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/articles/A5_data_graphics_files/crosstalk-1.2.1/scss/crosstalk.scss
docs/articles/A5_data_graphics_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/A5_data_graphics_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/A5_data_graphics_files/plotly-binding-4.10.4/plotly.js
docs/articles/A5_data_graphics_files/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
docs/articles/A5_data_graphics_files/plotly-main-2.11.1/plotly-latest.min.js
docs/articles/A5_data_graphics_files/typedarray-0.1/typedarray.min.js
docs/articles/A6_standardization.html
docs/articles/A6_standardization_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/B1_global.html
docs/articles/B1_global_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/B2_table_plus_geo.html
docs/articles/B2_table_plus_geo_files/Proj4Leaflet-1.0.1/proj4leaflet.js
docs/articles/B2_table_plus_geo_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/B2_table_plus_geo_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/B2_table_plus_geo_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/B2_table_plus_geo_files/leaflet-1.3.1/images/layers-2x.png
docs/articles/B2_table_plus_geo_files/leaflet-1.3.1/images/layers.png
docs/articles/B2_table_plus_geo_files/leaflet-1.3.1/images/marker-icon-2x.png
docs/articles/B2_table_plus_geo_files/leaflet-1.3.1/images/marker-icon.png
docs/articles/B2_table_plus_geo_files/leaflet-1.3.1/images/marker-shadow.png
docs/articles/B2_table_plus_geo_files/leaflet-1.3.1/leaflet.css
docs/articles/B2_table_plus_geo_files/leaflet-1.3.1/leaflet.js
docs/articles/B2_table_plus_geo_files/leaflet-binding-2.2.2/leaflet.js
docs/articles/B2_table_plus_geo_files/leaflet-providers-2.0.0/leaflet-providers_2.0.0.js
docs/articles/B2_table_plus_geo_files/leaflet-providers-plugin-2.2.2/leaflet-providers-plugin.js
docs/articles/B2_table_plus_geo_files/leafletfix-1.0.0/leafletfix.css
docs/articles/B2_table_plus_geo_files/proj4-2.6.2/proj4.min.js
docs/articles/B2_table_plus_geo_files/rstudio_leaflet-1.3.1/images/1px.png
docs/articles/B2_table_plus_geo_files/rstudio_leaflet-1.3.1/rstudio_leaflet.css
docs/articles/B3_counties.html
docs/articles/B3_counties_files/Proj4Leaflet-1.0.1/proj4leaflet.js
docs/articles/B3_counties_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/B3_counties_files/crosstalk-1.2.1/css/crosstalk.min.css
docs/articles/B3_counties_files/crosstalk-1.2.1/js/crosstalk.js
docs/articles/B3_counties_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/articles/B3_counties_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/articles/B3_counties_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/articles/B3_counties_files/crosstalk-1.2.1/scss/crosstalk.scss
docs/articles/B3_counties_files/datatables-binding-0.33/datatables.js
docs/articles/B3_counties_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/B3_counties_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
docs/articles/B3_counties_files/dt-core-1.13.6/css/jquery.dataTables.min.css
docs/articles/B3_counties_files/dt-core-1.13.6/js/jquery.dataTables.min.js
docs/articles/B3_counties_files/figure-html/lkd5-1.png
docs/articles/B3_counties_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/B3_counties_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/B3_counties_files/leaflet-1.3.1/images/layers-2x.png
docs/articles/B3_counties_files/leaflet-1.3.1/images/layers.png
docs/articles/B3_counties_files/leaflet-1.3.1/images/marker-icon-2x.png
docs/articles/B3_counties_files/leaflet-1.3.1/images/marker-icon.png
docs/articles/B3_counties_files/leaflet-1.3.1/images/marker-shadow.png
docs/articles/B3_counties_files/leaflet-1.3.1/leaflet.css
docs/articles/B3_counties_files/leaflet-1.3.1/leaflet.js
docs/articles/B3_counties_files/leaflet-binding-2.2.2/leaflet.js
docs/articles/B3_counties_files/leaflet-providers-2.0.0/leaflet-providers_2.0.0.js
docs/articles/B3_counties_files/leaflet-providers-plugin-2.2.2/leaflet-providers-plugin.js
docs/articles/B3_counties_files/leafletfix-1.0.0/leafletfix.css
docs/articles/B3_counties_files/proj4-2.6.2/proj4.min.js
docs/articles/B3_counties_files/rstudio_leaflet-1.3.1/images/1px.png
docs/articles/B3_counties_files/rstudio_leaflet-1.3.1/rstudio_leaflet.css
docs/articles/C1_body_overall.html
docs/articles/C1_body_overall_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/C1_body_overall_files/crosstalk-1.2.1/css/crosstalk.min.css
docs/articles/C1_body_overall_files/crosstalk-1.2.1/js/crosstalk.js
docs/articles/C1_body_overall_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/articles/C1_body_overall_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/articles/C1_body_overall_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/articles/C1_body_overall_files/crosstalk-1.2.1/scss/crosstalk.scss
docs/articles/C1_body_overall_files/datatables-binding-0.33/datatables.js
docs/articles/C1_body_overall_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/C1_body_overall_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
docs/articles/C1_body_overall_files/dt-core-1.13.6/css/jquery.dataTables.min.css
docs/articles/C1_body_overall_files/dt-core-1.13.6/js/jquery.dataTables.min.js
docs/articles/C1_body_overall_files/figure-html/dopl1-1.png
docs/articles/C1_body_overall_files/figure-html/dopl1-2.png
docs/articles/C1_body_overall_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/C1_body_overall_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/C2_variation_survival.html
docs/articles/C2_variation_survival_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/C2_variation_survival_files/figure-html/show1-1.png
docs/articles/C2_variation_survival_files/figure-html/show2-1.png
docs/articles/C2_variation_survival_files/figure-html/show3-1.png
docs/articles/C2_variation_survival_files/figure-html/show4-1.png
docs/articles/C3_subtypes_molecular.html
docs/articles/C3_subtypes_molecular_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/D1_clin_trial_concepts.html
docs/articles/D1_clin_trial_concepts_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/D2_equipoise.html
docs/articles/D2_equipoise_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/D3_randomization_bias.html
docs/articles/D3_randomization_bias_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/D4_comparing_trt.html
docs/articles/D4_comparing_trt_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/D4_comparing_trt_files/crosstalk-1.2.1/css/crosstalk.min.css
docs/articles/D4_comparing_trt_files/crosstalk-1.2.1/js/crosstalk.js
docs/articles/D4_comparing_trt_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/articles/D4_comparing_trt_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/articles/D4_comparing_trt_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/articles/D4_comparing_trt_files/crosstalk-1.2.1/scss/crosstalk.scss
docs/articles/D4_comparing_trt_files/datatables-binding-0.33/datatables.js
docs/articles/D4_comparing_trt_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/D4_comparing_trt_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
docs/articles/D4_comparing_trt_files/dt-core-1.13.6/css/jquery.dataTables.min.css
docs/articles/D4_comparing_trt_files/dt-core-1.13.6/js/jquery.dataTables.min.js
docs/articles/D4_comparing_trt_files/figure-html/doconf-1.png
docs/articles/D4_comparing_trt_files/figure-html/doplot-1.png
docs/articles/D4_comparing_trt_files/figure-html/dosummmm-1.png
docs/articles/D4_comparing_trt_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/D4_comparing_trt_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/E1_heidelberg2022.html
docs/articles/E1_heidelberg2022_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/E2_YESAI_2024.html
docs/articles/E2_YESAI_2024_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/custom.css
docs/articles/images/CNAdup.jpg
docs/articles/images/COSMICCNA.jpg
docs/articles/images/IARCoverall.jpg
docs/articles/images/SEERFEMALE.jpg
docs/articles/images/SEERMALE.jpg
docs/articles/images/SEERlist.jpg
docs/articles/images/bodymap.jpg
docs/articles/images/breastTTN.jpg
docs/articles/images/centralDogma.jpg
docs/articles/images/chromosomes.jpg
docs/articles/images/clearGDC.png
docs/articles/images/colon.jpg
docs/articles/images/colon8GroupIncidence.jpg
docs/articles/images/gdscnSchema.jpg
docs/articles/images/genecounts.jpg
docs/articles/images/genomeBrowser.jpg
docs/articles/images/introhisto.jpg
docs/articles/images/introseer.jpg
docs/articles/images/loose.jpg
docs/articles/images/lymExpanded.png
docs/articles/images/lymphlogic.png
docs/articles/images/marthEvolve.jpg
docs/articles/images/marthPatient.jpg
docs/articles/images/oncogridBRCA.jpg
docs/articles/images/oncotreeSNIP.jpg
docs/articles/images/pancreas.jpg
docs/articles/images/piecharts.jpg
docs/articles/images/rateOverview.jpg
docs/articles/images/shahGenomeWide.jpg
docs/articles/images/standardPopGraphs.jpg
docs/articles/images/tight.jpg
docs/articles/images/triangle.jpg
docs/articles/images/vantveerHeat.jpg
docs/articles/images/yescure.jpg
docs/articles/images/yespkgdown.jpg
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/MA_cancer_rate_table.html
docs/reference/Rplot001.png
docs/reference/SEER_2018.html
docs/reference/brcamutSE.html
docs/reference/build_deck.html
docs/reference/build_simple_survival_curve.html
docs/reference/build_surv_for_mut-1.png
docs/reference/build_surv_for_mut.html
docs/reference/canada_crude.html
docs/reference/cancer_map_app.html
docs/reference/cancer_map_usa.html
docs/reference/cancer_map_world.html
docs/reference/compare_tumors-1.png
docs/reference/compare_tumors.html
docs/reference/do_new_surv.html
docs/reference/faces.html
docs/reference/figures/CNAdup.jpg
docs/reference/figures/COSMICCNA.jpg
docs/reference/figures/Cancer_Data_Science_Topics.png
docs/reference/figures/ColoRectalUSACounty.jpg
docs/reference/figures/IARCoverall.jpg
docs/reference/figures/MassachusettsCountiesMap.jpg
docs/reference/figures/SEERFEMALE.jpg
docs/reference/figures/SEERMALE.jpg
docs/reference/figures/SEERlist.jpg
docs/reference/figures/YESCDS_map.png
docs/reference/figures/bodymap.jpg
docs/reference/figures/brainGeneralGDC.jpg
docs/reference/figures/brainIDH.jpg
docs/reference/figures/breastGenGDC.jpg
docs/reference/figures/breastTTN.jpg
docs/reference/figures/centralDogma.jpg
docs/reference/figures/chromosomes.jpg
docs/reference/figures/clearGDC.png
docs/reference/figures/colon.jpg
docs/reference/figures/colon8GroupIncidence.jpg
docs/reference/figures/ct_gov_disclaim.jpg
docs/reference/figures/dendbuild.jpg
docs/reference/figures/genecounts.jpg
docs/reference/figures/genomeBrowser.jpg
docs/reference/figures/iris.jpg
docs/reference/figures/loose.jpg
docs/reference/figures/lymExpanded.png
docs/reference/figures/lymphlogic.png
docs/reference/figures/marthEvolve.jpg
docs/reference/figures/marthPatient.jpg
docs/reference/figures/oncogridBRCA.jpg
docs/reference/figures/oncotreeSNIP.jpg
docs/reference/figures/pancreas.jpg
docs/reference/figures/piecharts.jpg
docs/reference/figures/rateOverview.jpg
docs/reference/figures/shahGenomeWide.jpg
docs/reference/figures/standardPopGraphs.jpg
docs/reference/figures/statesOverallMap.jpg
docs/reference/figures/tight.jpg
docs/reference/figures/vantveerHeat.jpg
docs/reference/figures/vikAsthmaUSA.jpg
docs/reference/figures/vikFrench.jpg
docs/reference/filter_woncan.html
docs/reference/full_house.html
docs/reference/get_hcc_spatial_path.html
docs/reference/has_mut_in.html
docs/reference/index.html
docs/reference/is_flush.html
docs/reference/libs/Proj4Leaflet-1.0.1/proj4leaflet.js
docs/reference/libs/crosstalk-1.2.1/css/crosstalk.min.css
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.js
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.js.map
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.min.js
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/reference/libs/crosstalk-1.2.1/scss/crosstalk.scss
docs/reference/libs/htmlwidgets-1.6.4/htmlwidgets.js
docs/reference/libs/leaflet-1.3.1/images/layers-2x.png
docs/reference/libs/leaflet-1.3.1/images/layers.png
docs/reference/libs/leaflet-1.3.1/images/marker-icon-2x.png
docs/reference/libs/leaflet-1.3.1/images/marker-icon.png
docs/reference/libs/leaflet-1.3.1/images/marker-shadow.png
docs/reference/libs/leaflet-1.3.1/leaflet.css
docs/reference/libs/leaflet-1.3.1/leaflet.js
docs/reference/libs/leaflet-binding-2.2.2/leaflet.js
docs/reference/libs/leaflet-providers-2.0.0/leaflet-providers_2.0.0.js
docs/reference/libs/leaflet-providers-plugin-2.2.2/leaflet-providers-plugin.js
docs/reference/libs/leafletfix-1.0.0/leafletfix.css
docs/reference/libs/plotly-binding-4.10.4/plotly.js
docs/reference/libs/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
docs/reference/libs/plotly-main-2.11.1/plotly-latest.min.js
docs/reference/libs/proj4-2.6.2/proj4.min.js
docs/reference/libs/rstudio_leaflet-1.3.1/images/1px.png
docs/reference/libs/rstudio_leaflet-1.3.1/rstudio_leaflet.css
docs/reference/libs/typedarray-0.1/typedarray.min.js
docs/reference/make_comparison.html
docs/reference/make_hist.html
docs/reference/make_pair.html
docs/reference/map_app.html
docs/reference/mass_cancer_map.html
docs/reference/mass_map.html
docs/reference/metabric.html
docs/reference/one_pair.html
docs/reference/ordered_seg_cal.html
docs/reference/plot.two_sample_mut_surv.html
docs/reference/plot_seer_trend-1.png
docs/reference/plot_seer_trend.html
docs/reference/plotwci-1.png
docs/reference/plotwci.html
docs/reference/print.two_sample_mut_surv.html
docs/reference/prostate_met_adeno.html
docs/reference/show_5y_estimate.html
docs/reference/show_median_estimate.html
docs/reference/statcrunch_msa.html
docs/reference/suits.html
docs/reference/summary.two_sample_mut_surv.html
docs/reference/table_woncan.html
docs/reference/two_pairs.html
docs/reference/two_sample_surv_setup-1.png
docs/reference/two_sample_surv_setup.html
docs/reference/url_1R.html
docs/reference/url_6NR.html
docs/reference/us_county_geo.html
docs/reference/us_map.html
docs/reference/variation_app.html
docs/reference/vjc_cancer_net.html
docs/reference/woncan.html
docs/reference/woncan_meta.html
docs/reference/woncan_types.html
docs/reference/world_cancer_2020_all.html
docs/reference/world_geo_sf.html
docs/sitemap.xml
inst/AIapp/server.R
inst/AIapp/ui.R
inst/cancer_map/server.R
inst/cancer_map/ui.R
inst/csv/CountyMapMASS.csv
inst/csv/CountyMapMASSCI.csv
inst/csv/MABreastWCI.csv
inst/csv/MASSProstateWCI.csv
inst/csv/README.txt
inst/csv/california_lung_statecancerprof.csv
inst/csv/world2020MFALL.csv
inst/csv/worldBrain2020Female55plus.csv
inst/csv/worldBrain2020MF55plus.csv
inst/csv/worldBrain2020MFALL.csv
inst/csv/worldBrain2020Male55plus.csv
inst/ipynb/.Rprofile
inst/ipynb/.ipynb_checkpoints/A1_cancer_table-checkpoint.ipynb
inst/ipynb/.ipynb_checkpoints/A2_rates-checkpoint.ipynb
inst/ipynb/.ipynb_checkpoints/A3_monitoring-checkpoint.ipynb
inst/ipynb/.ipynb_checkpoints/A4_interactive_tables-checkpoint.ipynb
inst/ipynb/.ipynb_checkpoints/A5_data_graphics-checkpoint.ipynb
inst/ipynb/.ipynb_checkpoints/A6_standardization-checkpoint.ipynb
inst/ipynb/.ipynb_checkpoints/B1_global-checkpoint.ipynb
inst/ipynb/.ipynb_checkpoints/B2_table_plus_geo-checkpoint.ipynb
inst/ipynb/.ipynb_checkpoints/B3_counties-checkpoint.ipynb
inst/ipynb/A0_intro_notebook.ipynb
inst/ipynb/A1_cancer_table.ipynb
inst/ipynb/A2_rates.ipynb
inst/ipynb/A3_monitoring.ipynb
inst/ipynb/A4_interactive_tables.ipynb
inst/ipynb/A5_data_graphics.ipynb
inst/ipynb/A6_standardization.ipynb
inst/ipynb/B1_global.ipynb
inst/ipynb/B2_table_plus_geo.ipynb
inst/ipynb/B3_counties.ipynb
inst/ipynb/C1_body_overall.ipynb
inst/ipynb/C2_variation_survival.ipynb
inst/ipynb/C3_subtypes_molecular.ipynb
inst/ipynb/D1_clin_trial_concepts.ipynb
inst/ipynb/D2_equipoise.ipynb
inst/ipynb/D3_randomization_bias.ipynb
inst/ipynb/D4_comparing_trt.ipynb
inst/ipynb/cnv-heatmap.html
inst/ipynb/common.Rprofile
inst/ipynb/images/CNAdup.jpg
inst/ipynb/images/COSMICCNA.jpg
inst/ipynb/images/Cancer_Data_Science_Topics.png
inst/ipynb/images/ColoRectalUSACounty.jpg
inst/ipynb/images/IARCoverall.jpg
inst/ipynb/images/MassachusettsCountiesMap.jpg
inst/ipynb/images/SEERFEMALE.jpg
inst/ipynb/images/SEERMALE.jpg
inst/ipynb/images/SEERlist.jpg
inst/ipynb/images/bodymap.jpg
inst/ipynb/images/brainGeneralGDC.jpg
inst/ipynb/images/brainIDH.jpg
inst/ipynb/images/breastGenGDC.jpg
inst/ipynb/images/breastTTN.jpg
inst/ipynb/images/centralDogma.jpg
inst/ipynb/images/chromosomes.jpg
inst/ipynb/images/clearGDC.png
inst/ipynb/images/colon.jpg
inst/ipynb/images/colon8GroupIncidence.jpg
inst/ipynb/images/ct_gov_disclaim.jpg
inst/ipynb/images/dendbuild.jpg
inst/ipynb/images/genecounts.jpg
inst/ipynb/images/genomeBrowser.jpg
inst/ipynb/images/introhisto.jpg
inst/ipynb/images/introseer.jpg
inst/ipynb/images/iris.jpg
inst/ipynb/images/loose.jpg
inst/ipynb/images/lymExpanded.png
inst/ipynb/images/lymphlogic.png
inst/ipynb/images/marthEvolve.jpg
inst/ipynb/images/marthPatient.jpg
inst/ipynb/images/oncogridBRCA.jpg
inst/ipynb/images/oncotreeSNIP.jpg
inst/ipynb/images/pancreas.jpg
inst/ipynb/images/piecharts.jpg
inst/ipynb/images/rateOverview.jpg
inst/ipynb/images/shahGenomeWide.jpg
inst/ipynb/images/standardPopGraphs.jpg
inst/ipynb/images/statesOverallMap.jpg
inst/ipynb/images/tight.jpg
inst/ipynb/images/vantveerHeat.jpg
inst/json/tensent.json
inst/map_app/server.R
inst/map_app/ui.R
inst/pamphlets/C1.pdf
inst/pamphlets/Csnap.jpg
inst/pamphlets/flyer.pdf
inst/pamphlets/galax1.jpg
inst/pamphlets/sep2022.Rmd
inst/pamphlets/yescds.bib
inst/scripts/Makefile
inst/scripts/pub_files/A0_intro_notebook.Rmd
inst/scripts/pub_files/A0_intro_notebook.ipynb
inst/scripts/pub_files/A0_intro_notebook.md
inst/scripts/pub_files/A1_cancer_table.Rmd
inst/scripts/pub_files/A1_cancer_table.ipynb
inst/scripts/pub_files/A1_cancer_table.md
inst/scripts/pub_files/A2_rates.Rmd
inst/scripts/pub_files/A2_rates.ipynb
inst/scripts/pub_files/A2_rates.md
inst/scripts/pub_files/A3_monitoring.Rmd
inst/scripts/pub_files/A3_monitoring.ipynb
inst/scripts/pub_files/A3_monitoring.md
inst/scripts/pub_files/A4_interactive_tables.Rmd
inst/scripts/pub_files/A4_interactive_tables.ipynb
inst/scripts/pub_files/A4_interactive_tables.md
inst/scripts/pub_files/A5_data_graphics.Rmd
inst/scripts/pub_files/A5_data_graphics.ipynb
inst/scripts/pub_files/A5_data_graphics.md
inst/scripts/pub_files/A6_standardization.Rmd
inst/scripts/pub_files/A6_standardization.ipynb
inst/scripts/pub_files/A6_standardization.md
inst/scripts/pub_files/B1_global.Rmd
inst/scripts/pub_files/B1_global.ipynb
inst/scripts/pub_files/B1_global.md
inst/scripts/pub_files/B2_table_plus_geo.Rmd
inst/scripts/pub_files/B2_table_plus_geo.ipynb
inst/scripts/pub_files/B2_table_plus_geo.md
inst/scripts/pub_files/B3_counties.Rmd
inst/scripts/pub_files/B3_counties.ipynb
inst/scripts/pub_files/B3_counties.md
inst/scripts/pub_files/C1_body_overall.Rmd
inst/scripts/pub_files/C1_body_overall.ipynb
inst/scripts/pub_files/C1_body_overall.md
inst/scripts/pub_files/C2_variation_survival.Rmd
inst/scripts/pub_files/C2_variation_survival.ipynb
inst/scripts/pub_files/C2_variation_survival.md
inst/scripts/pub_files/C3_subtypes_molecular.Rmd
inst/scripts/pub_files/C3_subtypes_molecular.ipynb
inst/scripts/pub_files/C3_subtypes_molecular.md
inst/scripts/pub_files/D1_clin_trial_concepts.Rmd
inst/scripts/pub_files/D1_clin_trial_concepts.ipynb
inst/scripts/pub_files/D1_clin_trial_concepts.md
inst/scripts/pub_files/D2_equipoise.Rmd
inst/scripts/pub_files/D2_equipoise.ipynb
inst/scripts/pub_files/D2_equipoise.md
inst/scripts/pub_files/D3_randomization_bias.Rmd
inst/scripts/pub_files/D3_randomization_bias.ipynb
inst/scripts/pub_files/D3_randomization_bias.md
inst/scripts/pub_files/D4_comparing_trt.Rmd
inst/scripts/pub_files/D4_comparing_trt.ipynb
inst/scripts/pub_files/D4_comparing_trt.md
inst/spatial_app/hcc1hires.png
inst/spatial_app/hccnr6he.png
inst/spatial_app/jour6nr.png
inst/spatial_app/key.png
inst/spatial_app/newjour1.png
inst/spatial_app/server.R
inst/spatial_app/stapp.R
inst/spatial_app/stapp2.R
inst/spatial_app/ui.R
inst/stapp/.Rhistory
inst/stapp/rsconnect/shinyapps.io/vjcitn/ratevariation.dcf
inst/stapp/server.R
inst/stapp/ui.R
inst/txt/USPR_Cancer_stats_wonder_1999_2018.txt
jupyter-galaxy-Dockerfile
man/MA_cancer_rate_table.Rd
man/SEER_2018.Rd
man/brcamutSE.Rd
man/build_deck.Rd
man/build_simple_survival_curve.Rd
man/build_surv_for_mut.Rd
man/canada_crude.Rd
man/cancer_map_app.Rd
man/cancer_map_usa.Rd
man/cancer_map_world.Rd
man/compare_tumors.Rd
man/do_new_surv.Rd
man/faces.Rd
man/figures/._Cancer_Data_Science_Topics.png
man/figures/CNAdup.jpg
man/figures/COSMICCNA.jpg
man/figures/Cancer_Data_Science_Topics.png
man/figures/ColoRectalUSACounty.jpg
man/figures/IARCoverall.jpg
man/figures/MassachusettsCountiesMap.jpg
man/figures/SEERFEMALE.jpg
man/figures/SEERMALE.jpg
man/figures/SEERlist.jpg
man/figures/YESCDS_map.png
man/figures/bodymap.jpg
man/figures/brainGeneralGDC.jpg
man/figures/brainIDH.jpg
man/figures/breastGenGDC.jpg
man/figures/breastTTN.jpg
man/figures/centralDogma.jpg
man/figures/chromosomes.jpg
man/figures/clearGDC.png
man/figures/colon.jpg
man/figures/colon8GroupIncidence.jpg
man/figures/ct_gov_disclaim.jpg
man/figures/dendbuild.jpg
man/figures/genecounts.jpg
man/figures/genomeBrowser.jpg
man/figures/iris.jpg
man/figures/loose.jpg
man/figures/lymExpanded.png
man/figures/lymphlogic.png
man/figures/marthEvolve.jpg
man/figures/marthPatient.jpg
man/figures/oncogridBRCA.jpg
man/figures/oncotreeSNIP.jpg
man/figures/pancreas.jpg
man/figures/piecharts.jpg
man/figures/rateOverview.jpg
man/figures/shahGenomeWide.jpg
man/figures/standardPopGraphs.jpg
man/figures/statesOverallMap.jpg
man/figures/tight.jpg
man/figures/vantveerHeat.jpg
man/figures/vikAsthmaUSA.jpg
man/figures/vikFrench.jpg
man/filter_woncan.Rd
man/full_house.Rd
man/get_hcc_spatial_path.Rd
man/is_flush.Rd
man/make_comparison.Rd
man/make_hist.Rd
man/make_pair.Rd
man/map_app.Rd
man/mass_cancer_map.Rd
man/mass_map.Rd
man/metabric.Rd
man/one_pair.Rd
man/ordered_seg_cal.Rd
man/plot_seer_trend.Rd
man/plotwci.Rd
man/prostate_met_adeno.Rd
man/show_5y_estimate.Rd
man/show_median_estimate.Rd
man/statcrunch_msa.Rd
man/suits.Rd
man/table_woncan.Rd
man/two_pairs.Rd
man/url_1R.Rd
man/url_6NR.Rd
man/us_county_geo.Rd
man/us_map.Rd
man/variation_app.Rd
man/vjc_cancer_net.Rd
man/woncan.Rd
man/woncan_meta.Rd
man/woncan_types.Rd
man/world_cancer_2020_all.Rd
man/world_geo_sf.Rd
vignettes/A0_intro_notebook.Rmd
vignettes/A1_cancer_table.Rmd
vignettes/A2_rates.Rmd
vignettes/A3_monitoring.Rmd
vignettes/A4_interactive_tables.Rmd
vignettes/A5_data_graphics.Rmd
vignettes/A6_standardization.Rmd
vignettes/B1_global.Rmd
vignettes/B2_table_plus_geo.Rmd
vignettes/B3_counties.Rmd
vignettes/C1_body_overall.Rmd
vignettes/C2_variation_survival.Rmd
vignettes/C3_subtypes_molecular.Rmd
vignettes/D1_clin_trial_concepts.Rmd
vignettes/D2_equipoise.Rmd
vignettes/D3_randomization_bias.Rmd
vignettes/D4_comparing_trt.Rmd
vignettes/E1_heidelberg2022.Rmd
vignettes/E2_YESAI_2024.Rmd
vignettes/cnv-heatmap.html
vignettes/curve.R
vignettes/custom.css
vignettes/images/CNAdup.jpg
vignettes/images/COSMICCNA.jpg
vignettes/images/Cancer_Data_Science_Topics.png
vignettes/images/ColoRectalUSACounty.jpg
vignettes/images/IARCoverall.jpg
vignettes/images/MassachusettsCountiesMap.jpg
vignettes/images/SEERFEMALE.jpg
vignettes/images/SEERMALE.jpg
vignettes/images/SEERlist.jpg
vignettes/images/bodymap.jpg
vignettes/images/brainGeneralGDC.jpg
vignettes/images/brainIDH.jpg
vignettes/images/breastGenGDC.jpg
vignettes/images/breastTTN.jpg
vignettes/images/centralDogma.jpg
vignettes/images/chromosomes.jpg
vignettes/images/clearGDC.png
vignettes/images/colon.jpg
vignettes/images/colon8GroupIncidence.jpg
vignettes/images/ct_gov_disclaim.jpg
vignettes/images/dendbuild.jpg
vignettes/images/gdscnSchema.jpg
vignettes/images/genecounts.jpg
vignettes/images/genomeBrowser.jpg
vignettes/images/introhisto.jpg
vignettes/images/introseer.jpg
vignettes/images/iris.jpg
vignettes/images/loose.jpg
vignettes/images/lymExpanded.png
vignettes/images/lymphlogic.png
vignettes/images/marthEvolve.jpg
vignettes/images/marthPatient.jpg
vignettes/images/oncogridBRCA.jpg
vignettes/images/oncotreeSNIP.jpg
vignettes/images/pancreas.jpg
vignettes/images/piecharts.jpg
vignettes/images/rateOverview.jpg
vignettes/images/shahGenomeWide.jpg
vignettes/images/standardPopGraphs.jpg
vignettes/images/statesOverallMap.jpg
vignettes/images/tight.jpg
vignettes/images/triangle.jpg
vignettes/images/vantveerHeat.jpg
vignettes/images/yescure.jpg
vignettes/images/yespkgdown.jpg
vignettes/rand.R
