R包
计算生物学
生物导体
算法
参考基因组
DNA测序
人工智能
Python(编程语言)
集合(抽象数据类型)
作者
Shanwen Sun,Lei Xu,Quan Zou,Guohua Wang
出处
期刊:Bioinformatics
[Oxford University Press]
日期:2021-06-09
卷期号:37 (9): 1319-1321
被引量:46
标识
DOI:10.1093/bioinformatics/btaa832
摘要
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 data are available at Bioinformatics online.
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