The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.
The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.
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DOI：
10.1093/bioinformatics/btx143
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发表时间：
2017-07-15
期刊：
影响因子：
--
通讯作者：
Brazma A
中科院分区：
文献类型：
--
作者：
Petryszak R;Fonseca NA;Füllgrabe A;Huerta L;Keays M;Tang YA;Brazma A
公开可获得的RNA测序(RNA-Seq)数据的指数增长对希望发现、分析和存储此类数据的研究人员提出了越来越大的挑战，特别是那些基于有限计算资源的机构的数据。EMBL-EBI处于一个理想的位置来应对这些挑战，让科学界不仅可以方便地获取原始数据，而且还可以方便地获取经过处理的RNA-Seq数据。我们提供了一个Web服务来访问系统和持续更新的标准化比对的结果，以及所有公共批量(在不久的将来还包括单细胞)RNA-Seq运行在欧洲核苷酸档案中的264个物种的基因和外显子表达的量化，使用代表性状态转移。RNAseq-er API(应用编程接口)支持基于本体的搜索和检索CRAM、Bigwig和bedGraph文件、基因和外显子表达量化矩阵(每百万个片段映射的每千个外显子片段、每百万个转录片段的片段数、原始计数)以及用本体术语注释的样本属性。到目前为止，在近1万项研究中(1PB的原始FASTQ数据)，超过2700个RNA-Seq运行在ENA的264个物种中，并通过API进行处理和提供。可以在http://www.ebi.ac.uk/fg/rnaseq/api.上访问RNAseq-er API用于分析数据的命令可在补充材料和https://github.com/nunofonseca/irap/wiki/iRAP-single-library.上找到补充数据可在生物信息学在线上获得。
The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer. The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API. The RNASeq-er API can be accessed at http://www.ebi.ac.uk/fg/rnaseq/api. The commands used to analyse the data are available in supplementary materials and at https://github.com/nunofonseca/irap/wiki/iRAP-single-library. Supplementary data are available at Bioinformatics online.
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影响因子：
14.9
作者：
Howe KL;Bolt BJ;Cain S;Chan J;Chen WJ;Davis P;Done J;Down T;Gao S;Grove C;Harris TW;Kishore R;Lee R;Lomax J;Li Y;Muller HM;Nakamura C;Nuin P;Paulini M;Raciti D;Schindelman G;Stanley E;Tuli MA;Van Auken K;Wang D;Wang X;Williams G;Wright A;Yook K;Berriman M;Kersey P;Schedl T;Stein L;Sternberg PW
通讯作者：
Sternberg PW
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Kolesnikov N;Hastings E;Keays M;Melnichuk O;Tang YA;Williams E;Dylag M;Kurbatova N;Brandizi M;Burdett T;Megy K;Pilicheva E;Rustici G;Tikhonov A;Parkinson H;Petryszak R;Sarkans U;Brazma A
通讯作者：
Brazma A
影响因子：
14.9
作者：
Silvester N;Alako B;Amid C;Cerdeño-Tárraga A;Cleland I;Gibson R;Goodgame N;Ten Hoopen P;Kay S;Leinonen R;Li W;Liu X;Lopez R;Pakseresht N;Pallreddy S;Plaister S;Radhakrishnan R;Rossello M;Senf A;Smirnov D;Toribio AL;Vaughan D;Zalunin V;Cochrane G
通讯作者：
Cochrane G
DOI：
10.1093/bioinformatics/btt547
发表时间：
2013-12-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cokelaer T;Pultz D;Harder LM;Serra-Musach J;Saez-Rodriguez J
通讯作者：
Saez-Rodriguez J