The regions of interest in such analyses are genes, transcripts, enhancers or many other types of sequence intervals that can be identified by their genomic coordinates. Bioconductor supports representation and analysis of genomic intervals with a “Ranges” infrastructure that encompasses data structures, algorithms and utilities including arithmetic functions, set operations and summarization [4] (Fig. 1). It consists of several packages including IRanges, GenomicRanges, GenomicAlignments, GenomicFeatures, VariantAnnotation and rtracklayer. The packages are frequently updated for functionality, performance and usability. The Ranges infrastructure was designed to provide tools that are convenient for end users analyzing data while retaining flexibility to serve as a foundation for the development of more complex and specialized software. We have formalized the data structures to the point that they enable interoperability, but we have also made them adaptable to specific use cases by allowing additional, less formalized user-defined data components such as application-defined annotation.
