Differential Enrichment analysis of Proteomics data
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Documentation for package ‘DEP’ version 1.22.0
Help Pages
| DEP-package | DEP: A package for Differential Enrichment analysis of Proteomics data. |
| add_rejections | Mark significant proteins |
| analyze_dep | Differential expression analysis |
| DEP | DEP: A package for Differential Enrichment analysis of Proteomics data. |
| DiUbi | DiUbi - Ubiquitin interactors for different diubiquitin-linkages (UbIA-MS dataset) |
| DiUbi_ExpDesign | Experimental design of the DiUbi dataset |
| filter_missval | Filter on missing values |
| filter_proteins | Filter proteins based on missing values |
| get_df_long | Generate a long data.frame from a SummarizedExperiment |
| get_df_wide | Generate a wide data.frame from a SummarizedExperiment |
| get_prefix | Obtain the longest common prefix |
| get_results | Generate a results table |
| get_suffix | Obtain the longest common suffix |
| import_IsobarQuant | Import from IsobarQuant |
| import_MaxQuant | Import from MaxQuant |
| impute | Impute missing values |
| LFQ | LFQ workflow |
| make_se | Data.frame to SummarizedExperiment object conversion using an experimental design |
| make_se_parse | Data.frame to SummarizedExperiment object conversion using parsing from column names |
| make_unique | Make unique names |
| manual_impute | Imputation by random draws from a manually defined distribution |
| meanSdPlot | Plot row standard deviations versus row means |
| normalize_vsn | Normalization using vsn |
| plot_all | Visualize the results in different types of plots |
| plot_cond | Plot frequency of significant conditions per protein and the overlap in proteins between conditions |
| plot_cond_freq | Plot frequency of significant conditions per protein |
| plot_cond_overlap | Plot conditions overlap |
| plot_cor | Plot correlation matrix |
| plot_coverage | Plot protein coverage |
| plot_detect | Visualize intensities of proteins with missing values |
| plot_dist | Plot Gower's distance matrix |
| plot_frequency | Plot protein overlap between samples |
| plot_gsea | Plot enriched Gene Sets |
| plot_heatmap | Plot a heatmap |
| plot_imputation | Visualize imputation |
| plot_missval | Plot a heatmap of proteins with missing values |
| plot_normalization | Visualize normalization |
| plot_numbers | Plot protein numbers |
| plot_pca | Plot PCA |
| plot_p_hist | Plot a P value histogram |
| plot_single | Plot values for a protein of interest |
| plot_volcano | Volcano plot |
| process | Proteomics data processing |
| report | Generate a markdown report |
| run_app | DEP shiny apps |
| se2msn | Deprecated Function to coerce SummarizedExperiment to MSnSet object |
| test_diff | Differential enrichment test |
| test_gsea | Gene Set Enrichment Analysis |
| theme_DEP1 | DEP ggplot theme 1 |
| theme_DEP2 | DEP ggplot theme 2 |
| TMT | TMT workflow |
| UbiLength | UbiLength - Ubiquitin interactors of different linear ubiquitin lengths (UbIA-MS dataset) |
| UbiLength_ExpDesign | Experimental design of the UbiLength dataset |