VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.
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DOI：
10.1186/s12859-018-2139-9
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发表时间：
2018-04-12
影响因子：
3
通讯作者：
Long HW
中科院分区：
文献类型：
--
作者：
Cornwell M;Vangala M;Taing L;Herbert Z;Köster J;Li B;Sun H;Li T;Zhang J;Qiu X;Pun M;Jeselsohn R;Brown M;Liu XS;Long HW
RNA测序已经成为一种普遍存在的技术，在整个生命科学中作为定量测量组织和细胞中RNA丰度的有效方法。RNA-seq技术使用的增加导致了从比对到下游途径分析的每一步分析的新工具的不断开发。然而，以可扩展和可重复的方式有效地使用这些分析工具可能具有挑战性，特别是对于非专家而言。使用工作流管理系统Snakemake，我们开发了一个用户友好，快速，高效和全面的RNA-seq分析管道。VIPER（Visualization Pipeline for RNA-seq analysis）是一种分析工作流程，它结合了一些最流行的工具，通过比对和质量控制，从原始测序数据进行RNA-seq分析，并进行下游差异表达和途径分析。VIPER是以模块化的方式创建的，以便快速整合新工具来扩展功能。这种能力已经被利用，包括最近开发的探索免疫浸润和T细胞CDR（互补决定区）重建能力的工具。管道已经被方便地打包，使得下载和安装VIPER使用的数十个软件包所需的计算技能最少。VIPER是一个全面的解决方案，可快速有效地执行大多数标准RNA-seq分析，并具有内置的定制和扩展能力。本文的在线版本（10.1186/s12859-018-2139-9）包含补充材料，可供授权用户使用。
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. The online version of this article (10.1186/s12859-018-2139-9) contains supplementary material, which is available to authorized users.
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影响因子：
5.8
作者：
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通讯作者：
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DOI：
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发表时间：
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期刊：
Bioinformatics (Oxford, England)
影响因子：
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