spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
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DOI：
10.1186/1471-2105-15-81
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发表时间：
2014-03-23
影响因子：
3
通讯作者：
Waage J
中科院分区：
文献类型：
--
作者：
Vitting-Seerup K;Porse BT;Sandelin A;Waage J
RNA-seq数据目前未得到充分利用，部分原因是难以预测替代转录事件对功能的影响。最近在全长转录本反褶积方面的软件改进促使我们开发了spliceR，这是一个用于分类备选剪接和预测编码潜力的R包。spliceR使用来自RNA-seq组装器的全长转录本输出来检测单个或多个外显子跳跃，替代供体和受体位点，内含子保留，替代第一个或最后一个外显子使用以及相互排斥的外显子事件。对于这些事件，spliceR还注释了不同剪接元件的基因组坐标，便于下游序列分析。对于每个转录异构体分数值计算，以确定转录切换之间的条件。最后，spliceR预测编码潜能，以及每个转录本潜在的无义介导衰变（NMD）敏感性。spliceR是一个易于使用的工具，通过允许更深入地注释RNA-seq数据，扩展了RNA-seq和组装技术的可用性。spliceR是作为一个R包实现的，可以从Bioconductor存储库（http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html）免费获得。
RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential. spliceR uses the full-length transcript output from RNA-seq assemblers to detect single or multiple exon skipping, alternative donor and acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. For each of these events spliceR also annotates the genomic coordinates of the differentially spliced elements, facilitating downstream sequence analysis. For each transcript isoform fraction values are calculated to identify transcript switching between conditions. Lastly, spliceR predicts the coding potential, as well as the potential nonsense mediated decay (NMD) sensitivity of each transcript. spliceR is an easy-to-use tool that extends the usability of RNA-seq and assembly technologies by allowing greater depth of annotation of RNA-seq data. spliceR is implemented as an R package and is freely available from the Bioconductor repository ( http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html).
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影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
14.9
作者：
Wang L;Park HJ;Dasari S;Wang S;Kocher JP;Li W
通讯作者：
Li W
DOI：
10.1093/bioinformatics/bts452
发表时间：
2012-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Ryan MC;Cleland J;Kim R;Wong WC;Weinstein JN
通讯作者：
Weinstein JN
影响因子：
48
作者：
Katz, Yarden;Wang, Eric T.;Airoldi, Edoardo M.;Burge, Christopher B.
通讯作者：
Burge, Christopher B.
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J