Introduction | Installation | rjags | beer | Simulated data | edgeR | BEER (Bayesian Estimation Enrichment in R) | Prior parameters | Removing super enriched peptides | Saving MCMC samples | Visualizing MCMC Convergence | Beads-only round robin | Parallelization | Plot Helpers | getExpected() | getBF() | sessionInfo()

Installation | Introduction | Components of a PhIPData Object | Accessing and modifying components of PhIPData object | Assays | Peptide metadata | Sample metadata | Experimental metadata | Common operations on PhIPData objects | Subsetting | PhIPData summaries | Using template libraries | Using aliases | Coercion from PhIPData to other containers | sessionInfo()