Enabled differential testing with missing values.
Added data.frame output functionality from plotting functions.
Enabled multi-SE plotting in plot_normalization() and plot_imputation().
Deprecated se2msn() and msn2se() functions. Use as('MSnSet') or as('SummarizedExperiment') from MSnbase package instead.
Added a vignette on missing value handling in DEP.
Added citation: Zhang, Smits, van Tilburg et al. Nature Protocols 2018.
First release of the DEP package for differential enrichment analysis of proteomics data.