Advantages and limits in the adoption of reproducible research and R-tools for the analysis of omic data

Reproducible (computational) Research is crucial to produce transparent and high quality scientific papers. First, we illustrate the benefits that scientific community can receive from the adoption of Reproducible Research standards in the analysis of high-throughput omic data. Then, we describe several tools useful to researchers to increase the reproducibility of their works. Moreover, we face the advantages and limits of reproducible research and how they could be addressed and solved. Overall, this paper should be considered as a proof of concept on how and what characteristic - in our opinion - should be considered to conduct a study in the spirit of Reproducible Research. Therefore, the scope of this paper is two-fold. The first goal consists in presenting and discussing some easy-to-use instruments for data analysts to promote reproducible research in their analyses. The second aim is to encourage developers to incorporate automatic reproducibility features in their tools.