RT Journal Article SR Electronic T1 PHESANT: a tool for performing automated phenome scans in UK Biobank JF bioRxiv FD Cold Spring Harbor Laboratory SP 111500 DO 10.1101/111500 A1 Louise A C Millard A1 Neil M Davies A1 Tom R Gaunt A1 George Davey Smith A1 Kate Tilling YR 2017 UL http://biorxiv.org/content/early/2017/02/26/111500.abstract AB Motivation Epidemiological cohorts typically contain a diverse set of phenotypes such that automation of phenome scans is non-trivial, because they require highly heterogeneous models. For this reason, phenome scans have to date tended to use a smaller homogeneous set of phenotypes that can be analysed in a consistent fashion. We present PHESANT (PHEnome Scan ANalysis Tool), a software package for performing comprehensive phenome scans in UK Biobank.General features PHESANT tests the association of a specified trait with all continuous, integer and categorical variables in UK Biobank, or a specified subset. PHESANT uses a novel rule-based algorithm to determine how to appropriately test each trait, then performs the analyses and produces plots and summary tables.Implementation The PHESANT phenome scan is implemented in R. PHESANT includes a novel Javascript D3.js visualization, and accompanying Java code that converts the phenome scan results to the required JavaScript Object Notation (JSON) format.AVAILABILITY PHESANT is available on GitHub at [https://github.com/MRCIEU/PHESANT]. Git tag v0.2 corresponds to the version presented here.