The seeker R package: simplified fetching and processing of transcriptome data.
The seeker R package: simplified fetching and processing of transcriptome data.
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作者：
Schoenbachler JL;Hughey JJ
转录组数据对于询问生物系统已经变得非常有价值。准备用于分析的转录组数据集，特别是RNA-seq数据集，需要多个步骤和软件程序，每个步骤都有自己的命令行界面(CLI)。尽管这些CLI功能强大，但它们通常需要外壳脚本来实现自动化和并行化，这可能会有很高的学习曲线，特别是当CLI的细节因工具而异时。然而，由于基于R的生物数据分析工具的过多和流行，许多从事转录组数据工作的人已经熟悉R。因此，我们开发了一个名为SEEKER的R包，用于简化RNA-seq和微阵列数据的获取和处理。Seeker是各种现有工具的包装器，它提供了标准接口、简单的并行化和详细的日志记录。Seeker的主要输出-基于Entrez或EnSembl基因ID的样本元数据和基因表达值-可以直接插入差异表达分析。为了最大限度地提高再现性，Seeker以独立的R包和包含所有依赖项的Docker映像的形式提供，两者均可从访问。
Transcriptome data have become invaluable for interrogating biological systems. Preparing a transcriptome dataset for analysis, particularly an RNA-seq dataset, entails multiple steps and software programs, each with its own command-line interface (CLI). Although these CLIs are powerful, they often require shell scripting for automation and parallelization, which can have a high learning curve, especially when the details of the CLIs vary from one tool to another. However, many individuals working with transcriptome data are already familiar with R due to the plethora and popularity of R-based tools for analyzing biological data. Thus, we developed an R package called seeker for simplified fetching and processing of RNA-seq and microarray data. Seeker is a wrapper around various existing tools, and provides a standard interface, simple parallelization, and detailed logging. Seeker’s primary output—sample metadata and gene expression values based on Entrez or Ensembl Gene IDs—can be directly plugged into a differential expression analysis. To maximize reproducibility, seeker is available as a standalone R package and in a Docker image that includes all dependencies, both of which are accessible at .
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影响因子：
14.9
作者：
Ritchie ME;Phipson B;Wu D;Hu Y;Law CW;Shi W;Smyth GK
通讯作者：
Smyth GK
DOI：
10.1126/science.1247651
发表时间：
2014-02-14
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jaitin DA;Kenigsberg E;Keren-Shaul H;Elefant N;Paul F;Zaretsky I;Mildner A;Cohen N;Jung S;Tanay A;Amit I
通讯作者：
Amit I
影响因子：
--
作者：
Soneson C;Love MI;Robinson MD
通讯作者：
Robinson MD
影响因子：
2.8
作者：
Stirling C;Andrews S;Croft T;Vickers J;Turner P;Robinson A
通讯作者：
Robinson A
影响因子：
2.1
作者：
Irizarry, RA;Hobbs, B;Speed, TP
通讯作者：
Speed, TP