Files in kuppal2/xmsPANDA

R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

R/E.W.k.R R/QRILCimpute.R R/RFimpute.R R/ROCinternal.panda.R R/W.k.R R/calc_stats.R R/calculate_concentration.R R/check_model.R R/compare.normalization.R R/confusion_matrix2.R R/data_preprocess.R R/degree_eval.R R/diffRank.R R/diffexp.R R/diffexp.biomarkers1.R R/diffexp.child.R R/diffexp.lite.R R/diffexpcoxph.R R/diffexplmonewayanovarepeat.R R/diffexplmreg.R R/diffexplmregrepeat.R R/diffexplmtwowayanova.R R/diffexplmtwowayanovarepeat.R R/diffexplogitreg.R R/diffexponewayanova.R R/diffexpsvmrfe.R R/diffexpsvmrfemulticlass.R R/diffrank_eval.R R/do_MSTUS_norm.R R/do_TIC_norm.R R/do_cor.R R/do_cubicspline_norm.R R/do_cv.R R/do_eigenms_norm.R R/do_loess_norm.R R/do_log2transform_norm.R R/do_mars.R R/do_mars_lmreg.R R/do_mean.R R/do_medcenter_norm.R R/do_minmax.R R/do_pamr.R R/do_paretoscaling_norm.R R/do_plsda.R R/do_plsda_rand.R R/do_quantile_norm.R R/do_rangescaling_norm.R R/do_rf.R R/do_rf_boruta.R R/do_rf_conditional.R R/do_ridge_lasso_elasticnet.R R/do_rsd.R R/do_sva_norm.R R/do_vsn_norm.R R/do_vst_norm_count.R R/do_wgcna.R R/do_znormtransform_norm.R R/docortest.R R/draw_keggmap.R R/eig_norm1.R R/eig_norm2.R R/eig_norm2test.R R/eval.class.acc1.R R/find.Overlapping.R R/find.Overlapping.mzs.R R/find.Unique.mzs.R R/generate_distribution.R R/generate_distribution_concentration.R R/getCorchild.R R/getSumreplicates.R R/getSumreplicateschild.R R/getVenn.R R/get_VIPmulticomp.R R/get_barplots.R R/get_biorep.cor.plots.R R/get_boxplot_colors.R R/get_boxplots.R R/get_boxplots_child.R R/get_bubbleplot.R R/get_classification.accuracy.R R/get_classification.accuracy.child.R R/get_classification.accuracy_vold.R R/get_data_summary.R R/get_diagnosis.R R/get_fcs.R R/get_fcs_child.R R/get_fdr_adjusted_pvalue.R R/get_fdr_adjusted_pvalue_child.R R/get_forestplot.R R/get_full_cormat.R R/get_hca.R R/get_hca_child.R R/get_hexcolors_for_palettes.R R/get_individualsampleplots.R R/get_kegg_compounds.R R/get_kegg_compounds_brite.R R/get_layout.R R/get_lineplots.R R/get_manhattanplots.R R/get_partial_cornet.R R/get_pca.R R/get_pcascoredistplots.R R/get_pcascoredistplots_child.R R/get_plscompvar.R R/get_plsplots.R R/get_roc.R R/get_scatter_plots.R R/get_spaghettiplots.R R/get_survivalanalysis.R R/get_survivalanalysis_univariate.R R/get_survplot_adjustedcurve.R R/get_volcanoplots.R R/ggadjustedcurves.average.R R/ggadjustedcurves.conditional.R R/ggadjustedcurves.marginal.R R/ggadjustedcurves.single.R R/imp_elim_proteins.R R/make.formula.string.R R/makeLMFormula.R R/metabnet.R R/mmul.R R/my.Psi.R R/my.Psi.dash.R R/mystar.R R/mytriangle.R R/nefs.R R/normalize.qspline.R R/outlier_detect.R R/pal_jama_custom.R R/pal_jco_custom.R R/pal_lancet_custom.R R/pal_nejm_custom.R R/pal_npg_custom.R R/phi.R R/plot.eigentrends.R R/plot.eigentrends.start.R R/plot.pairwise.correlation.R R/plot.pairwise.correlation.bipartite.R R/plotEigengeneNetworks_custom.R R/plotTukeyHSD1.R R/plot_graph.R R/plot_sample_correlation_child.R R/plsda_cv.R R/quant.R R/replace_outliers.R R/rnorm.trunc.R R/runApp.xmsPANDA.R R/runApp.xmsPANDALite.R R/runlmreg.R R/runlogitreg.R R/scale_colour_Publication.R R/scale_fill_Publication.R R/set_panel_size.R R/stratify_by_class.R R/sva.id.R R/svm.getweights.R R/svm_cv.R R/theme_Publication.R R/varimp_parallel.R R/view_color_img.R R/xmsPANDAv1.3.2-internal.R R/z.test.R inst/color_palettes_xmsPANDA.pdf inst/shinyapp/R/additional_analysis.R inst/shinyapp/R/data_preprocessing.R inst/shinyapp/R/graphical_options.R inst/shinyapp/R/help_page.R inst/shinyapp/R/input.R inst/shinyapp/R/introduction_page.R inst/shinyapp/R/load_packages.R inst/shinyapp/R/network_analysis.R inst/shinyapp/R/statistical_analysis_page.R inst/shinyapp/R/workflow.R inst/shinyapp/R/workflow2.r inst/shinyapp/dependencies.R inst/shinyapp/server.R inst/shinyapp/ui.R inst/shinyapp/www/xmsPANDA-manual.pdf inst/shinyappLite/R/additional_analysis.R inst/shinyappLite/R/data_preprocessing.R inst/shinyappLite/R/graphical_options.R inst/shinyappLite/R/help_page.R inst/shinyappLite/R/input.R inst/shinyappLite/R/introduction_page.R inst/shinyappLite/R/load_packages.R inst/shinyappLite/R/network_analysis.R inst/shinyappLite/R/statistical_analysis_page_lite.R inst/shinyappLite/R/steps.R inst/shinyappLite/R/workflow.R inst/shinyappLite/R/workflow2.r inst/shinyappLite/dependencies.R inst/shinyappLite/server.R inst/shinyappLite/ui.R inst/shinyappLite/www/xmsPANDA-manual.pdf inst/xmsPANDA-manual.pdf inst/xmsPANDA_example_script.R inst/xmsPANDA_v1.3_installation.R inst/xmsPANDAlite_example_script_classification.R inst/xmsPANDAlite_example_script_regression.R man/data_preprocess.Rd man/diffexp.Rd man/diffexp.lite.Rd man/do_wgcna.Rd man/get_boxplots.Rd man/get_classification.accuracy.Rd man/get_fcs.Rd man/get_hca.Rd man/get_manhattanplots.Rd man/get_pca.Rd man/get_pcascoredistplots.Rd man/get_roc.Rd man/get_volcanoplots.Rd man/metabnet.Rd man/runApp.xmsPANDA.Rd man/runApp.xmsPANDALite.Rd man/xmsPANDAv1.3-package.Rd