Man pages for DEP
Differential Enrichment analysis of Proteomics data

add_rejectionsMark significant proteins
analyze_depDifferential expression analysis
DEPDEP: A package for Differential Enrichment analysis of...
DiUbiDiUbi - Ubiquitin interactors for different...
DiUbi_ExpDesignExperimental design of the DiUbi dataset
filter_missvalFilter on missing values
filter_proteinsFilter proteins based on missing values
get_df_longGenerate a long data.frame from a SummarizedExperiment
get_df_wideGenerate a wide data.frame from a SummarizedExperiment
get_prefixObtain the longest common prefix
get_resultsGenerate a results table
get_suffixObtain the longest common suffix
import_IsobarQuantImport from IsobarQuant
import_MaxQuantImport from MaxQuant
imputeImpute missing values
LFQLFQ workflow
make_seData.frame to SummarizedExperiment object conversion using an...
make_se_parseData.frame to SummarizedExperiment object conversion using...
make_uniqueMake unique names
manual_imputeImputation by random draws from a manually defined...
meanSdPlotPlot row standard deviations versus row means
normalize_vsnNormalization using vsn
plot_allVisualize the results in different types of plots
plot_condPlot frequency of significant conditions per protein and the...
plot_cond_freqPlot frequency of significant conditions per protein
plot_cond_overlapPlot conditions overlap
plot_corPlot correlation matrix
plot_coveragePlot protein coverage
plot_detectVisualize intensities of proteins with missing values
plot_distPlot Gower's distance matrix
plot_frequencyPlot protein overlap between samples
plot_gseaPlot enriched Gene Sets
plot_heatmapPlot a heatmap
plot_imputationVisualize imputation
plot_missvalPlot a heatmap of proteins with missing values
plot_normalizationVisualize normalization
plot_numbersPlot protein numbers
plot_pcaPlot PCA
plot_p_histPlot a P value histogram
plot_singlePlot values for a protein of interest
plot_volcanoVolcano plot
processProteomics data processing
reportGenerate a markdown report
run_appDEP shiny apps
se2msnDeprecated Function to coerce SummarizedExperiment to MSnSet...
test_diffDifferential enrichment test
test_gseaGene Set Enrichment Analysis
theme_DEP1DEP ggplot theme 1
theme_DEP2DEP ggplot theme 2
TMTTMT workflow
UbiLengthUbiLength - Ubiquitin interactors of different linear...
UbiLength_ExpDesignExperimental design of the UbiLength dataset
DEP documentation built on Aug. 10, 2019, 2 a.m.