# TraianProt: a user-friendly R package for wide format proteomics data downstream analysis

## Documentation for package ‘TraianProt’ version 0.99.16

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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
traianprot_power_curve | Create power curve
traian_to_SE | Export TraianProt results to SummarizedExperiment
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