Peer Review #2 of "beadplexr: reproducible and automated analysis of multiplex bead assays (v0.1)"

Multiplex bead assays are an extension of the commonly used sandwich ELISA.The advantage over ELISA is that they make simultaneous evaluation of several analytes possible.Several commercial assay systems, where the beads are acquired on a standard flow cytometer, exist.These assay systems come with their own software tool for analysis and evaluation of the concentration of the analyzed analytes.However, these tools are either tied to particular commercial software or impose other limitations to their licenses, such as the number of events which can be analyzed.In addition, all these solutions are 'point and click' which potentially obscures the steps taken in the analysis.Here we present beadplexer, an open-source R-package for the reproducible analysis of multiplex bead assay data.The package makes it possible to automatically identify bead clusters, and provides functionality to easily fit a standard curve and calculate the concentrations of the analyzed analytes.beadplexer is available from CRAN and from https://gitlab.com/ustervbo/beadplexr