Automated analysis of small RNA datasets with RAPID

Sivarajan Karunanithi, Martin Simon, Marcel H. Schulz
<span title="2019-04-10">2019</span> <i title="PeerJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eyfkjqp7sva5bbnwatk5zazi7q" style="color: black;">PeerJ</a> </i> &nbsp;
Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present
more &raquo; ... RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2. Availability and Implementation RAPID is available under MIT license at https://github.com/SchulzLab/RAPID. We recommend using it as a conda environment available from https://anaconda.org/bioconda/rapid
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj.6710">doi:10.7717/peerj.6710</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30993044">pmid:30993044</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6462184/">pmcid:PMC6462184</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/62bhqpotavew3cpuxfpywududa">fatcat:62bhqpotavew3cpuxfpywududa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426093324/https://peerj.com/articles/6710.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3f/13/3f134c47b1a3b488770574caf5ff8b0ff7fdb29b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj.6710"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462184" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>