PEBBA is a webtool that performs Over Representation Analysis (ORA) to determine whether pre-defined sets of genes and pathways are present more than would be expected in a subset of your differential expression data.
You will need to upload 2 files to run a PEBBA analysis: a DEG file and a GMT file. For your convenience we make available 2 common GMT files, so you actually only need to provide a GMT file if you would like to use your own custom file.
Selecting the correct parameters for your over representation analysis may be a challenging task, by slightly tuning your parameters you may arrive at vastly different and contradictory results. PEBBA tackles this issue by first ranking genes by both statistical significance and biological importance through the use of pi values an then analysing the results of a range of parameters instead of a single handpicked parameter combination. This meta analysis approach of looking at the parameter space empowers the user to trace more precise conclusions about its data. For more details about the inner workings of PEBBA you may refer to our paper or to its open source implentation.