Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by selective enrichment of sequences with desirable properties followed by quantification by sequencing.mutscanis an R package for flexible analysis of such experiments, covering the entire workflow from raw reads up to statistical analysis and visualization. The core components are implemented in C++ for efficiency. Various experimental designs are supported, including single or paired reads with optional unique molecular identifiers. To find variants with changed relative abundance,mutscanemploys established statistical models provided in theedgeRandlimmapackages.mutscanis available fromhttps://github.com/fmicompbio/mutscan.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13059-023-02967-0.