基于快速自举的 RNA-Seq 数据表达水平和差异表达的置信区间估计。
Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data.
机构信息
Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA.
Immunology Department, University of Connecticut Health Center, Farmington, CT 06030, USA.
出版信息
Bioinformatics. 2017 Oct 15;33(20):3302-3304. doi: 10.1093/bioinformatics/btx365.
SUMMARY
This note presents IsoEM2 and IsoDE2, new versions with enhanced features and faster runtime of the IsoEM and IsoDE packages for expression level estimation and differential expression. IsoEM2 estimates fragments per kilobase million (FPKM) and transcript per million (TPM) levels for genes and isoforms with confidence intervals through bootstrapping, while IsoDE2 performs differential expression analysis using the bootstrap samples generated by IsoEM2. Both tools are available with a command line interface as well as a graphical user interface (GUI) through wrappers for the Galaxy platform.
AVAILABILITY AND IMPLEMENTATION
The source code of this software suite is available at https://github.com/mandricigor/isoem2. The Galaxy wrappers are available at https://toolshed.g2.bx.psu.edu/view/saharlcc/isoem2_isode2/.
CONTACT
imandric1@student.gsu.edu or ion@engr.uconn.edu.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
概述
本文介绍了 IsoEM2 和 IsoDE2，这两个新版本增强了 IsoEM 和 IsoDE 软件包的功能，并提高了运行速度，可用于表达水平估计和差异表达分析。IsoEM2 通过自举法为基因和异构体估计片段每兆碱基百万 (FPKM) 和每百万转录物 (TPM) 水平，并通过 IsoEM2 生成的自举样本进行差异表达分析。这两个工具都提供了命令行界面以及通过 Galaxy 平台的包装器提供的图形用户界面 (GUI)。
可用性和实现
该软件套件的源代码可在 https://github.com/mandricigor/isoem2 上获得。Galaxy 包装器可在 https://toolshed.g2.bx.psu.edu/view/saharlcc/isoem2_isode2/ 上获得。
联系人
imandric1@student.gsu.edu 或 ion@engr.uconn.edu。
补充信息
补充数据可在 Bioinformatics 在线获得。
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