Abstract

Summary

Processing raw reads of RNA-sequencing (RNA-seq) data, no matter public or newly sequenced data, involves a lot of specialized tools and technical configurations that are often unfamiliar and time-consuming to learn for non-bioinformatics researchers. Here, we develop the R package BP4RNAseq, which integrates the state-of-art tools from both alignment-based and alignment-free quantification workflows. The BP4RNAseq package is a highly automated tool using an optimized pipeline to improve the sensitivity and accuracy of RNA-seq analyses. It can take only two non-technical parameters and output six formatted gene expression quantification at gene and transcript levels. The package applies to both retrospective and newly generated bulk RNA-seq data analyses and is also applicable for single-cell RNA-seq analyses. It, therefore, greatly facilitates the application of RNA-seq.

Availability and implementation

The BP4RNAseq package for R and its documentation are freely available at https://github.com/sunshanwen/BP4RNAseq.

Supplementary information

Supplementary dataSupplementary data are available at Bioinformatics online.

中文翻译：

---

BP4RNAseq：使用基于对齐和无对齐的量化方法进行回顾性和新生成的 RNA-seq 数据分析的保姆包

摘要

概括

处理 RNA 测序 (RNA-seq) 数据的原始读数，无论是公共数据还是新测序数据，都涉及许多专门的工具和技术配置，对于非生物信息学研究人员来说，这些工具和技术配置通常不熟悉且耗时。在这里，我们开发了 R 包 BP4RNAseq，它集成了基于对齐和无对齐的量化工作流程的最新工具。BP4RNAseq 包是一种高度自动化的工具，它使用优化的管道来提高 RNA-seq 分析的灵敏度和准确性。它可以只需要两个非技术参数，并在基因和转录水平上输出六种格式化的基因表达量化。该软件包适用于回顾性和新生成的大量 RNA-seq 数据分析，也适用于单细胞 RNA-seq 分析。因此，它

可用性和实施

R 的 BP4RNAseq 包及其文档可在 https://github.com/sunshanwen/BP4RNAseq 上免费获得。

补充资料

补充数据补充数据可在生物信息学在线获得。