QuagmiR: a cloud-based application for isomiR big data analytics
QuagmiR: a cloud-based application for isomiR big data analytics
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DOI：
10.1093/bioinformatics/bty843
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发表时间：
2019-05-01
期刊：
影响因子：
5.8
通讯作者：
Gu, Shuo
中科院分区：
文献类型：
--
作者：
Bofill-De Ros, Xavier;Chen, Kevin;Gu, Shuo
microRNAs（miRNAs）是基因表达的主要调控因子。最近的研究表明，miRNA异构体（isomiRs）在癌症发展中发挥着独特的作用。在这里，我们介绍了QuagmiR，这是第一个基于云的工具，用于分析来自下一代测序数据的isomiR。QuagmiR使用一种新颖而灵活的搜索算法，旨在检测和注释异构异构体，它允许广泛定制查询过程和参考数据库，以满足用户的不同研究需求。可用性和实现QuagmiR是用Python编写的，可以从GitHub（https：//github.com/Gu-Lab-RBL-NCI/QuagmiR）免费获得。QuagmiR可以在本地机器上从命令行运行，也可以在高性能服务器上运行。该工具的网络可访问版本也可通过国家癌症研究所资助的七桥癌症基因组学云（https：//www.example.com）供学术研究人员使用。补充信息补充数据可在生物信息学在线获得。cancergenomicscloud.org
MicroRNAs (miRNAs) function as master regulators of gene expression. Recent studies demonstrate that miRNA isoforms (isomiRs) play a unique role in cancer development. Here, we present QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designed for the detection and annotation of heterogeneous isomiRs, it permits extensive customization of the query process and reference databases to meet the user's diverse research needs.Availability and implementation QuagmiR is written in Python and can be obtained freely from GitHub (https://github.com/Gu-Lab-RBL-NCI/QuagmiR). QuagmiR can be run from the command line on local machines, as well as on high-performance servers. A web-accessible version of the tool has also been made available for use by academic researchers through the National Cancer Institute-funded Seven Bridges Cancer Genomics Cloud (https://cancergenomicscloud.org).Supplementary informationSupplementary data are available at Bioinformatics online.