期刊
BIOINFORMATICS
卷 37, 期 9, 页码 1319-1321出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btaa832
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类别
资金
- National Key R&D Program of China [2018YFC0910405]
- National Natural Science Foundation of China [61922020, 61771165, 91935302]
BP4RNAseq is an R package that integrates state-of-the-art tools to improve sensitivity and accuracy of RNA-seq analysis, suitable for processing both bulk and single-cell RNA-seq data.
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.
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