Popularity and performance of bioinformatics software: The case of gene set analysis

In this 2021 paper published in BMC Bioinformatics, Xie et al. examine big omics and gene set analysis, a common analytical technique for bioinformaticists. The authors argue that biomedical science researchers have not been using the best GSA methods among those that are actually available. They chose to conduct research of popularity and performance based on prior described validation strategies and existing benchmark studies. Noting that popular methods are not always the best methods, the authors conclude with five points from their research, including a need for deeper discussions and research about GSA methods and more rigorous validation procedures for GSA tools. They also provide examples of evaluational tools for GSA and other bioinformatics software.

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