Differential Enrichment analysis of Proteomics data

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Documentation for package ‘DEP’ version 1.31.0

• 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