We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method.
- 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.
- Subjects
RNA sequencing; DATA analysis; GENE expression; BABYSITTERS; PIPELINE inspection; PREDICATE calculus
- Publication
Bioinformatics, 2021, Vol 37, Issue 9, p1319
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btaa832