BioConductor: Microarray versus Next-Generation Sequencing toolsets

Abstract

Both microarray and next generation sequencing platforms generate copious amounts of data for each experiment. Thus, computational tools are required to handle and process such experiments. For microarray analysis, many open-source R packages have been developed, most of which are available through the BioConduc- tor project. With certain microarray plat- forms, it is now possible to perform the entire analysis chain using only BioConductor tools. A comprehensive next-generation sequencing toolchain in pure R/BioConductor has until so far not been possible. Next-generation sequencing analysis still requires the use of disparate tools on disparate platforms: only some of them in R. This literature review reviewed the existing BioConductor toolsets for both approaches, and highlights key differences and similari- ties.