Files in kazeera/hourglass
This Package Provides Visualizations of Annotated Numeric Data
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
NAMESPACE
R/AAA_importFrom.R
R/FC.pval.R
R/average.R
R/boxplot.R
R/cluster.R
R/colors.R
R/corrplot.R
R/corrscatt.R
R/create_plots.R
R/discrete_barplot.R
R/feat_sets.R
R/get_objects_run_hourglass.R
R/heatmap.R
R/het_barplot.R
R/impute_w_mean.R
R/make_dataset_ob.R
R/paired.R
R/profile_barplot.R
R/remove_outliers.R
R/run_comparisons.R
R/run_hourglass.R
R/sort.R
R/stats.R
R/subset.R
R/survival.R
R/utils.R
R/utils_files.R
README.md
data/LEVELS.RData
data/PANC_TISS_ORDER.RData
data/example_IHC_samples_dataset.RData
data/example_IHC_samples_run.RData
docs/how-to-use-the-desktop-application.html
docs/how-to-use-the-r-package.html
docs/images/Hourglass_art.PNG
docs/images/Hourglass_logo-removebg.png
docs/images/R_functions.png
docs/images/annotations.png
docs/images/app/GUI_0_overview.png
docs/images/app/GUI_1_welcome.png
docs/images/app/GUI_2_upload-data1.png
docs/images/app/GUI_2_upload-data2.png
docs/images/app/GUI_2_upload-data3.png
docs/images/app/GUI_2_upload-data4_go-back.png
docs/images/app/GUI_3_pick-comparisons1.png
docs/images/app/GUI_3_pick-comparisons2.png
docs/images/app/GUI_4_1_select-columns2.png
docs/images/app/GUI_4_2_pick-params1.png
docs/images/app/GUI_4_2_pick-params2.png
docs/images/app/GUI_4_3_define-sets1.png
docs/images/app/GUI_4_3_define-sets2.png
docs/images/app/GUI_5_adv-options1.png
docs/images/app/GUI_5_adv-options2.png
docs/images/app/GUI_5_adv-options3_colors.png
docs/images/app/GUI_6_customize-colors1.png
docs/images/app/GUI_6_customize-colors2.png
docs/images/app/GUI_7_run-hourglass1.png
docs/images/app/GUI_7_run-hourglass2.png
docs/images/contributors1.png
docs/images/contributors11.PNG
docs/images/contributors2.png
docs/images/contributors21.PNG
docs/images/excel/output-excel_colors.png
docs/images/excel/output-excel_comparisons.png
docs/images/excel/output-excel_feature-parameters.png
docs/images/excel/output-excel_feature-sets.png
docs/images/features_vs_parameters2.png
docs/images/input_files.JPG
docs/images/levels_of_analysis.png
docs/images/making_row_annotations.png
docs/images/output_overview.png
docs/images/overall_inputoutput.png
docs/images/patients_vs_samples.png
docs/images/plots/QC feature.PNG
docs/images/plots/QC parameter.PNG
docs/images/plots/boxplot indiv.PNG
docs/images/plots/boxplot overview.PNG
docs/images/plots/correlation scatter.PNG
docs/images/plots/correlation.PNG
docs/images/plots/discrete barplot.PNG
docs/images/plots/example/boxplot indiv ex.PNG
docs/images/plots/heatmap expression.PNG
docs/images/plots/heatmap pval FC.PNG
docs/images/plots/hetplot filled.PNG
docs/images/plots/hetplot stacked.PNG
docs/images/plots/id_table.PNG
docs/images/plots/paired.PNG
docs/images/plots/profile barplot filled.PNG
docs/images/plots/profile barplot stacked.PNG
docs/images/plots/survival.PNG
docs/images/workflow.JPG
docs/index.html
docs/input-data.html
docs/installation.html
docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css
docs/libs/anchor-sections-1.1.0/anchor-sections.css
docs/libs/anchor-sections-1.1.0/anchor-sections.js
docs/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
docs/libs/gitbook-2.6.7/css/plugin-bookdown.css
docs/libs/gitbook-2.6.7/css/plugin-clipboard.css
docs/libs/gitbook-2.6.7/css/plugin-fontsettings.css
docs/libs/gitbook-2.6.7/css/plugin-highlight.css
docs/libs/gitbook-2.6.7/css/plugin-search.css
docs/libs/gitbook-2.6.7/css/plugin-table.css
docs/libs/gitbook-2.6.7/css/style.css
docs/libs/gitbook-2.6.7/js/app.min.js
docs/libs/gitbook-2.6.7/js/clipboard.min.js
docs/libs/gitbook-2.6.7/js/jquery.highlight.js
docs/libs/gitbook-2.6.7/js/lunr.js
docs/libs/gitbook-2.6.7/js/plugin-bookdown.js
docs/libs/gitbook-2.6.7/js/plugin-clipboard.js
docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js
docs/libs/gitbook-2.6.7/js/plugin-search.js
docs/libs/gitbook-2.6.7/js/plugin-sharing.js
docs/libs/header-attrs-2.14/header-attrs.js
docs/libs/jquery-2.2.3/jquery.min.js
docs/output-plot-types.html
docs/search_index.json
docs/what-is-hourglass.html
example/1_make_dataset_vals.R
example/2_make_dataset_ann.R
example/3_surv_plot.R
example/4_make_other_objects.R
example/5_run_Hg.R
example/5_test.R
example/ExampleData2/Example_IHC_sample_colAnn.csv
example/ExampleData2/Example_IHC_sample_rowAnn.csv
example/ExampleData2/Example_IHC_sample_vals.csv
example/ExampleData2/example_IHC_samples_dataset.RData
example/ExampleData2/example_IHC_samples_run.RData
example/Example_IHC_sample_Information.xlsx
example/Example_IHC_sample_UserOptions.xlsx
example/LEVELS.RData
example/PANC_TISS_ORDER.RData
example/Template_UserOptions.xlsx
example/Tutorial Markdown.Rmd
example/ds_core_example.rds
hourglass.Rproj
man/add_to_rowAnn.Rd
man/as_numeric_factor.Rd
man/avg_dataframe.Rd
man/avg_dataset.Rd
man/bin_vars.Rd
man/clean_colors.Rd
man/cluster_corrmat.Rd
man/cluster_df.Rd
man/create_folder.Rd
man/create_plots.Rd
man/create_plots_helper.Rd
man/df_to_numeric.Rd
man/evaluate_filter.Rd
man/get_ann_colors.Rd
man/get_col_gradient.Rd
man/get_col_palette.Rd
man/get_colors.Rd
man/get_comparison_name.Rd
man/get_comparisons.Rd
man/get_datasets.Rd
man/get_duplicated_cases.Rd
man/get_element_colors.Rd
man/get_feat_sets.Rd
man/get_file.Rd
man/get_levels.Rd
man/get_nth_part.Rd
man/get_outliers.Rd
man/get_paired_ds.Rd
man/get_rowAnn_color_pal.Rd
man/has_at.least_n.vals.Rd
man/has_less.than.eq.to_NA.thres.Rd
man/impute_ds.Rd
man/impute_w_mean.Rd
man/impute_w_mean_df.Rd
man/load_packages.Rd
man/make.unique.2.Rd
man/make_FC.pval_df.Rd
man/make_FC.pval_df_helper.Rd
man/make_FC.pval_plot.Rd
man/make_dataset_ob.Rd
man/means_of_groups.Rd
man/medians_of_groups.Rd
man/perform_t.test.Rd
man/perform_wilcox.Rd
man/plot_corrplot.Rd
man/plot_corrplotgg.Rd
man/plot_discrete_barplot.Rd
man/plot_heatmap.Rd
man/plot_het_barplot.Rd
man/plot_indiv_boxplot.Rd
man/plot_indiv_corrscatt.Rd
man/plot_indiv_paired.Rd
man/plot_overview_boxplot.Rd
man/plot_overview_corr_scatt.Rd
man/plot_profile_barplot.Rd
man/plot_surv_curve.Rd
man/print_unique_elements_count.Rd
man/pval_to_stars.Rd
man/read_file.Rd
man/reform_ann_df.Rd
man/remove_outliers.Rd
man/remove_outliers2.Rd
man/remove_outliers_df.Rd
man/rename_column.Rd
man/run_comparison.Rd
man/run_comparison_helper.Rd
man/run_corrplot_analysis.Rd
man/run_discrete_barplot_analysis.Rd
man/run_from_excel.Rd
man/run_het_analysis.Rd
man/run_hourglass.Rd
man/run_paired_analysis.Rd
man/run_profile_barplot.Rd
man/run_surv_analysis.Rd
man/save_table.Rd
man/sort_dataframe.Rd
man/sort_dataset.Rd
man/split_one.by.one.Rd
man/subset_by_filters.Rd
man/subset_dataframe.Rd
man/subset_dataset.Rd
man/subset_feat_sets_ds.Rd
man/test_Hourglass.Rd
man/trim_each_part.Rd
man/turn_off_null_devices.Rd
