机构：[1]Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.[2]Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.[3]Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA.[4]Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany.[5]University of Massachusetts Medical School, Worcester, MA 01655, USA.[6]Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA.[7]Department of Bioinformatics, School of Life Sciences, Tongji University, Shanghai 200092, China.[8]State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.[9]Beijing Institute of Basic Medical Sciences, Beijing, China.
RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.
Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses.
VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.
基金：
US National Institutes of Health [U01 CA180980] to MB and National Natural
Science Foundation of China [31329003] to XSL.
语种：
外文
PubmedID：
中科院(CAS)分区：
出版当年[2018]版：
大类|3 区生物
小类|2 区数学与计算生物学3 区生化研究方法3 区生物工程与应用微生物
最新[2023]版：
大类|3 区生物学
小类|3 区生化研究方法3 区数学与计算生物学4 区生物工程与应用微生物
第一作者：
第一作者机构：[1]Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
共同第一作者：
通讯作者：
通讯机构：[1]Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.[2]Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
推荐引用方式(GB/T 7714)：
MacIntosh Cornwell,Mahesh Vangala,Len Taing,et al.VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.[J].BMC bioinformatics.2018,19(1):135.doi:10.1186/s12859-018-2139-9.
APA：
MacIntosh Cornwell,Mahesh Vangala,Len Taing,Zachary Herbert,Johannes Köster...&Henry W. Long.(2018).VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis..BMC bioinformatics,19,(1)
MLA：
MacIntosh Cornwell,et al."VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.".BMC bioinformatics 19..1(2018):135
