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Representation and Manipulation of Genomic Tuples in R

GenomicTuples is an R/Bioconductor package (R Core Team 2016; Wolfgang Huber et al 2015) that defines general purpose containers for storing and manipulating genomic tuples. A genomic tuple of size m is of the form chromosome:strand:{pos_1, pos_2, ..., pos_m} where pos_1 < pos_2 < ... < pos_m are positions along the chromosome. The difference between a genomic tuple and a genomic range/interval is like that of a difference between an ordered set and an interval. For example, the genomic 2-tuple chr3:+:{65, 77} differs from the genomic range chr3:+:[65, 77] by not including any of the intervening loci, chr3:+:66 to chr3:+:76.