barplot_func            Create Bar Plot from Enrichment Results
boxplot_function        Create Boxplot of Sample Intensities
collapse_technical_replicates
                        Collapse Technical Replicates in Proteomics
                        Data
corrplot_function       Correlation Matrix
Diferential_boxplot     Differential Protein Boxplot
dotplot_func            Create Dot Plot from Enrichment Results
filter_valids           Filter proteins by valid values
gostplot_func           Manhattan Plot for Functional Enrichment
Goterms_finder          Find GO Terms (gprofiler2)
histogram               Plot a Histogram
identify_proteins       Identify Proteins
igraph_analysis         Perform igraph Analysis on STRING Subnetworks
impute_data             Impute Missing Values using Down-Shifted Normal
                        Distribution
impute_KNN_data         Impute missing data using k-NN
interactions_down       Plot STRING Interactions for Down-regulated
                        Proteins
interactions_up         Get STRING Interactions for Up-regulated
                        Proteins
median_centering        Perform median centering normalization
my_heatmap              Base R Heatmap
my_heatmap_differential
                        Differential Protein Heatmap (ggplot)
normalization_func      Apply Normalization to LOG2 Columns
obtain_LOG.names        Obtain LOG2 Column Names
obtain_unique_proteins
                        Obtain Unique Proteins Between Conditions
pca                     Custom PCA Plot (Base R)
plotCV2                 Plot Coefficient of Variation vs. Mean
postimputation_state    Plot Post-Imputation Density
preimputation_state     Plot Missingness Pattern
qqplot_function         Create a Q-Q Plot
quick_filtering         Quick Data Filtering
runTraianProt           Launch the TraianProt Shiny Application
scatterplot_function    Create a Scatterplot with Marginal Densities
statistical_analysis    Limma function for statistical analysis
traian_to_SE            Export TraianProt results to
                        SummarizedExperiment
traianprot_power_curve
                        Create power curve
tsne                    t-SNE Plot
unique_peptides_filter
                        Filter Proteins by Unique Peptide Counts
venn_diagram            Create a Venn Diagram
volcano_plot            This function generates an interactive volcano
                        plot using the 'plotly' package based on
                        differential expression results.
volcano_plot_tiff       Create a Static Volcano Plot for Publication
