Evaluating Genomic Range Joins using Streaming


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In this example, Bryan Lewis shows how the Streaming Interface can be used to evaluate range (aka overlap) joins between genomic variants and (in this case) exome regions. As an alternative to writing this computation as a SciDB operator, he simply wrote an R script that leverages the fast IRanges package from Bioconductor. Then SciDB streaming is used to easily invoke the script in parallel on SciDB data. Check it out! https://github.com/Paradigm4/stream/blob/master/r_pkg/vignettes/ranges.Rmd