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
LFQ                     LFQ workflow
TMT                     TMT workflow
UbiLength               UbiLength - Ubiquitin interactors of different
                        linear ubiquitin lengths (UbIA-MS dataset)
UbiLength_ExpDesign     Experimental design of the UbiLength dataset
add_rejections          Mark significant proteins
analyze_dep             Differential expression analysis
filter_missval          Filter 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
import_IsobarQuant      Import from IsobarQuant
import_MaxQuant         Import from MaxQuant
impute                  Impute missing values
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_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_p_hist             Plot a P value histogram
plot_pca                Plot PCA
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                  SummarizedExperiment to MSnSet object
                        conversion
test_diff               Differential enrichment test
test_gsea               Gene Set Enrichment Analysis
theme_DEP1              DEP ggplot theme 1
theme_DEP2              DEP ggplot theme 2
