EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK.
Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.
We present an R based pipeline, ArrayExpressHTS, for pre-processing, expression estimation and data quality assessment of high-throughput sequencing transcriptional profiling (RNA-seq) datasets. The pipeline starts from raw sequence files and produces standard Bioconductor R objects containing gene or transcript measurements for downstream analysis along with web reports for data quality assessment. It may be run locally on a user's own computer or remotely on a distributed R-cloud farm at the European Bioinformatics Institute. It can be used to analyse user's own datasets or public RNA-seq datasets from the ArrayExpress Archive.
The R package is available at www.ebi.ac.uk/tools/rcloud with online documentation at www.ebi.ac.uk/Tools/rwiki/, also available as supplementary material.
我们提出了一个基于 R 的管道，ArrayExpressHTS，用于预处理、表达估计和高通量测序转录谱（RNA-seq）数据集的数据质量评估。该管道从原始序列文件开始，生成包含基因或转录物测量值的标准 Bioconductor R 对象，用于下游分析，并提供数据质量评估的网络报告。它可以在用户自己的计算机上本地运行，也可以在欧洲生物信息学研究所的分布式 R 云农场远程运行。它可用于分析用户自己的数据集或来自 ArrayExpress 档案的公共 RNA-seq 数据集。
R 包可在 www.ebi.ac.uk/tools/rcloud 上获得，在线文档可在 www.ebi.ac.uk/Tools/rwiki/ 上获得，也可作为补充材料获得。
