Shanwen Sun1, Lei Xu2, Quan Zou1,3, Guohua Wang3,4. 1. Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054 China. 2. School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, 518055 China. 3. State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China. 4. College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040 China.
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 data are available at Bioinformatics online.
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.
Authors: Mahmood Barani; Mohammad Reza Hajinezhad; Saman Sargazi; Abbas Rahdar; Sheida Shahraki; Azadeh Lohrasbi-Nejad; Francesco Baino Journal: J Mater Sci Mater Med Date: 2021-12-04 Impact factor: 3.896