AUTHOR=Zou Jian , Düren Yannick , Qin Li-Xuan 

TITLE=PRECISION.seq: An R Package for Benchmarking Depth Normalization in microRNA Sequencing

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.823431

DOI=10.3389/fgene.2021.823431

ISSN=1664-8021

ABSTRACT=<p>We present a new R package <italic>PRECISION.seq</italic> for assessing the performance of depth normalization in microRNA sequencing data. It provides a pair of microRNA sequencing data sets for the same set of tumor samples, additional pairs of data sets simulated by re-sampling under various patterns of differential expression, and a collection of numerical and graphical tools for assessing the performance of normalization methods. Users can easily assess their chosen normalization method and compare its performance to nine methods already included in the package. <italic>PRECISION.seq</italic> enables an objective and systematic evaluation of normalization methods in microRNA sequencing using realistically distributed and robustly benchmarked data under a wide range of differential expression patterns. To our best knowledge, this is the first such tool available. The data sets and source code of the R package can be found at <ext-link ext-link-type="uri" xlink:href="https://github.com/LXQin/PRECISION.seq" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/LXQin/PRECISION.seq</ext-link>.</p>