1.22版本的变化- - - - - - - - - - - - - - - - - - - - - - - -以下添加了增强systemPipeR概述。——与升级提供了在本版本中,systemPipeR已成为一个更通用的数据分析工作流环境不再局限于分析门店数据。现在它可以有效地用于数据分析任务在很多组学领域,包括基因组学、蛋白质组学、代谢组学和药物发现。——一个工作流控制类(SYSargsList)允许用户管理添加了多工位的工作流程从一个容器。这种方式可以选择并执行多个工作流步骤与标准R语法构造子集,例如runWF [1:3]。——添加了各种改进systemPipeR新的命令行界面包括最近推出了SYSargs2类支持通用工作流语言(CWL)。——实用程序已经添加到可视化工作流设计和与不同的图形拓扑布局。——改进监控工作流的运行状况以及更好的跟踪警告和错误消息。这包括科学和技术状态报告的生成。1.3版本的变化- - - - - - - - - - - - - - - - - - - - - - - o systemPipeR概述是一个R / Bioconductor包来构建和运行自动化分析工作流广泛的下一代序列(上天)应用程序。 Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. o The most important enhancements in the upcoming release of the package are outlined below. NGS WORKFLOWS o Added new end-to-end workflows for 3 additional NGS application areas: - Ribo-Seq and polyRibo-Seq - ChIP-Seq - VAR-Seq The previous version of systemPipeR included only a complete workflow for RNA-Seq. o Added the data package 'systemPipeRdata' to generate systemPipeR workflow environments with a single command (genWorkenvir) containing all parameter files and sample data required to quickly test and run workflows. This change will also allow evaluation of much more code examples in the vignettes during the package build/test process than this was possible in the past. o About 20 new functions have been added to the package. Some examples are: - Read pre-processor function with support for SE and PE reads - Parallelization option of detailed FASTQ quality reports - Read distribution plots across all features available in a genome annotation (see ?featuretypeCounts) - Visualization of coverage trends along transcripts summarized for any number of transcripts (see ?featureCoverage) - Functionalities to predict uORFs/sORFs and to use them for expression profiling - Differential expression/binding analysis includes now DESeq2 as well as edgeR o Added param templates for additional command-line software including, but not limited to: BWA-MEM, GATK, BCFtools, MACS2 o Adoption of R Markdown for main vignette. Future plans are to provide for all workflows the report templates in both formats: Latex/PDF and R_Markdown/HTML. WORFLOW FRAMEWORK o Simplified design of complex analysis workflows. Workflows can now include any number or combination of R and/or command-line steps o Improvements to workflow automation and parallelization on single machines and computer clusters. This also includes now many additional parallelization examples in the workflow vignettes.