Files in DEP

Differential Enrichment analysis of Proteomics data

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