recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.
recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.
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DOI：
10.12688/f1000research.12223.1
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发表时间：
2017-01-01
期刊：
影响因子：
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通讯作者：
Jaffe, Andrew E
中科院分区：
文献类型：
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作者：
Collado-Torres, Leonardo;Nellore, Abhinav;Jaffe, Andrew E
recount2 资源由 70,000 多个统一处理的人类 RNA-seq 样本组成，涵盖 TCGA 和 SRA，包括 GTEx。处理后的数据可以通过 recount2 网站和 recount Bioconductor 包访问。此工作流程详细说明了如何使用 recount 包以及如何将其与其他 Bioconductor 包集成以进行可使用 recount2 资源执行的多项分析。特别是，我们描述了如何在 recount2 中计算覆盖计数矩阵以及获取公共元数据的不同方式，这可以促进下游分析。分步说明展示了如何进行基因水平差异表达分析、可视化基础水平基因组覆盖数据以及在多个特征水平上执行分析。因此，该工作流程提供了更多信息来理解 recount2 中的数据以及使用该数据的 R 代码纲要。
The recount2 resource is composed of over 70,000 uniformly processed human RNA-seq samples spanning TCGA and SRA, including GTEx. The processed data can be accessed via the recount2 website and the recount Bioconductor package. This workflow explains in detail how to use the recount package and how to integrate it with other Bioconductor packages for several analyses that can be carried out with the recount2 resource. In particular, we describe how the coverage count matrices were computed in recount2 as well as different ways of obtaining public metadata, which can facilitate downstream analyses. Step-by-step directions show how to do a gene-level differential expression analysis, visualize base-level genome coverage data, and perform an analyses at multiple feature levels. This workflow thus provides further information to understand the data in recount2 and a compendium of R code to use the data.