TraianProt: a user-friendly R package for wide format proteomics
data downstream analysis
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘TraianProt’ version 0.99.16
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 |