├── DESCRIPTION ├── NAMESPACE ├── R ├── DEP.R ├── data.R ├── enrichR_functions.R ├── functions.R ├── gg_theme.R ├── plot_functions_QC.R ├── plot_functions_explore.R ├── plot_functions_frequencies.R ├── plot_functions_results.R ├── run_app_function.R ├── sysdata.rda ├── workflow_functions.R ├── wrapper_functions.R └── zzz.R ├── README.md ├── data ├── DiUbi.rda ├── DiUbi_ExpDesign.rda ├── UbiLength.rda └── UbiLength_ExpDesign.rda ├── inst ├── CITATION ├── NEWS.Rd ├── Report.Rmd └── shiny_apps │ ├── LFQ │ └── app.R │ └── TMT │ └── app.R ├── man ├── DEP.Rd ├── DiUbi.Rd ├── DiUbi_ExpDesign.Rd ├── LFQ.Rd ├── TMT.Rd ├── UbiLength.Rd ├── UbiLength_ExpDesign.Rd ├── add_rejections.Rd ├── analyze_dep.Rd ├── filter_missval.Rd ├── filter_proteins.Rd ├── get_df_long.Rd ├── get_df_wide.Rd ├── get_prefix.Rd ├── get_results.Rd ├── get_suffix.Rd ├── import_IsobarQuant.Rd ├── import_MaxQuant.Rd ├── impute.Rd ├── make_se.Rd ├── make_se_parse.Rd ├── make_unique.Rd ├── manual_impute.Rd ├── meanSdPlot.Rd ├── normalize_vsn.Rd ├── plot_all.Rd ├── plot_cond.Rd ├── plot_cond_freq.Rd ├── plot_cond_overlap.Rd ├── plot_cor.Rd ├── plot_coverage.Rd ├── plot_detect.Rd ├── plot_dist.Rd ├── plot_frequency.Rd ├── plot_gsea.Rd ├── plot_heatmap.Rd ├── plot_imputation.Rd ├── plot_missval.Rd ├── plot_normalization.Rd ├── plot_numbers.Rd ├── plot_p_hist.Rd ├── plot_pca.Rd ├── plot_single.Rd ├── plot_volcano.Rd ├── process.Rd ├── report.Rd ├── run_app.Rd ├── se2msn.Rd ├── test_diff.Rd ├── test_gsea.Rd ├── theme_DEP1.Rd └── theme_DEP2.Rd ├── tests ├── testthat.R └── testthat │ ├── test_1_unique_SE.R │ ├── test_2_missVal_norm.R │ ├── test_3_imputation.R │ ├── test_4_differential_testing.R │ ├── test_5_plot_functions_results.R │ ├── test_6_plot_functions_QC.R │ ├── test_7_plot_functions_frequencies.R │ ├── test_8_plot_functions_explore.R │ ├── test_9_workflows.R │ ├── test_9a_wrapper.R │ └── test_shiny_app.R └── vignettes ├── DEP.Rmd └── MissingValues.Rmd /DESCRIPTION: 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