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[mRNA-seq] 你们听说过recount计划吗?

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发表于 2017-6-8 19:10:27 | 显示全部楼层 |阅读模式
本帖最后由 ydchen 于 2017-6-8 19:12 编辑

因为各种各样的表达数据太多了,有测序平台差异,实验材料差异,实验室数据处理pipeline差异。
这样大家得到的表达数据都不一样。

为了解决这个问题,推出了recount计划:

recount2: analysis-ready RNA-seq gene and exon counts datasets
https://jhubiostatistics.shinyapps.io/recount/

A multi-experiment resource of analysis-ready RNA-seq gene and exon count datasets
recount2 is an online resource consisting of RNA-seq gene and exon counts as well as coverage bigWig files for 2041 different studies. It is the second generation of the ReCount project. The raw sequencing data were processed with Rail-RNA as described in the recount2 paper and at Nellore et al, Genome Biology, 2016 which created the coverage bigWig files. For ease of statistical analysis, for each study we created count tables at the gene and exon levels and extracted phenotype data, which we provide in their raw formats as well as in RangedSummarizedExperiment R objects (described in the SummarizedExperiment Bioconductor package). We also computed the mean coverage per study and provide it in a bigWig file, which can be used with the derfinder Bioconductor package to perform annotation-agnostic differential expression analysis at the expressed regions-level as described at Collado-Torres et al, Genome Research, 2017. The count tables, RangedSummarizeExperiment objects, phenotype tables, sample bigWigs, mean bigWigs, and file information tables are ready to use and freely available here. We also created the recount Bioconductor package which allows you to search and download the data for a specific study . By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.
Related publicationsCollado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Reproducible RNA-seq analysis using recount2. Nature Biotechnology, 2017. doi: 10.1038/nbt.3838.




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发表于 2017-10-12 08:22:17 | 显示全部楼层
今天参加学校的Genomics and Bioinformatics Symposium, 这篇文章的第三作者Ellis SE介绍的就是recount2, 看起来很不错。
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