Exploration, analysis and visualization of Cufflinks high-throughput RNA-Seq data
CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
High-throughput sequencing of RNA-fragments is a powerful technique that has many applications, including but not limited to transcript assembly, qantitation, and differential expression analysis. The results of these analyses is often very large data sets with a high degree of relations between various data types and can be somewhat overwhelming. CummeRbund was designed to help simplify the analysis and exploration portion of RNA-Seq data derrived from the output of a differential expression analysis using cuffdiff with the goal of providing fast and intuitive access to your results.
CummeRbund takes the various output files from a cuffdiff run and creates a SQLite database of the results describing appropriate relationships betweeen genes, transcripts, transcription start sites, and CDS regions. Once stored and indexed, data for these features, even across multiple samples or conditions, can be retrieved very efficiently and allows the user to explore subfeatures of individual genes, or genesets as the analysis requires. We have implemented numerous plotting functions as well for commonly used visualizations. Check back often as we are constantly updating features.
CummeRbund创建了一个SQLite数据库，将cuffdiff运行产生的结果都存储到数据库中，将genes、transcripts、transcription start sites、以及CDS建立关联。将这些数据存储到数据库中，并建立相关的索引，就可以很容易的对多个样本之间或者其他条件的数据进行查询检索，允许用户对于单个或者一组基因的各种feature进行比较分析。同时还提供了诸多的绘图函数，可以满足一般的数据可视化需要。 继续阅读