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Updated: Dec 7, 2025
Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
Published on: February 2, 2024
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both
Shanwen Sun1, Lei Xu2, Quan Zou1,3
1Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054 China.
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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