Highly Interactive Data Analysis and Productivity (HIDAP) tools for Breeding

Plant breeders routinely work with large datasets that increasingly also add new levels of dimensionality and complexity using, for example, –omics data. This gives breeders additional work for data analysis, which can be addressed at least partially using computational tools. To some extent, field trials are routine and repetitive and can benefit from standardized reporting; high density data sets and complex relationships can benefit from visualization and visual navigation; and complex relationships can benefit from applying linked data concepts and interactivity. Here we apply a new generation of R based libraries to implement a custom platform (HIDAP) for productively handling such breeding data. The HIDAP platform consists of a set of R libraries addressing tasks like data quality control, basic analysis of single and multiple breeding trials, and integrating environmental, phenotypic and genomic data. It also creates printable reports based on modifiable and extensible templates. It can be used as a companion tool with software platforms like the Integrated Breeding Platform (IBP) and the Sweetpotatobase since it can directly exchange files with these two and exchange data in general via implementing the ‘Plant Breeding Application Programming Interface API’. Like R, the platform is fully open source and available across operating systems, and can be used offline and online. The libraries are available from a dedicated mini CRAN server, and can also be used individually.