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apmsWAPP: Pre- and Postprocessing for AP-MS data analysis based on spectral counts

apmsWAPP provides a complete workflow for the analysis of AP-MS data (replicate single-bait purifications including negative controls) based on spectral counts. It comprises pre-processing, scoring and postprocessing of protein interactions. A final list of interaction candidates is reported: it provides a ranking of the candidates according to their p-values which allow estimating the number of false-positive interactions.