# Differential Enrichment analysis of Proteomics data

## Documentation for package ‘DEP’ version 1.2.0

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

## 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