BingleSeq: A user-friendly R package for Bulk and Single-cell RNA-Seq Data Analysis

Abstract

RNA sequencing is a high-throughput sequencing technique considered as an indispensable research tool used in a broad range of transcriptome analysis studies. The most common application of RNA Sequencing is Differential Expression analysis and it is used to determine genetic loci with distinct expression across different conditions. On the other hand, an emerging field called single-cell RNA sequencing is used for transcriptome profiling at the individual cell level. The standard protocols for both these types of analyses include the processing of sequencing libraries and result in the generation of count matrices. An obstacle to these analyses and the acquisition of meaningful results is that both require programming expertise. BingleSeq was developed as an intuitive application that provides a user-friendly solution for the analysis of count matrices produced by both Bulk and Single-cell RNA-Seq experiments. This was achieved by building an interactive dashboard-like user interface and incorporating three state-of-the-art software packages for each type of the aforementioned analyses, alongside additional features such as key visualisation techniques, functional gene annotation analysis and rank-based consensus for differential gene analysis results, among others. As a result, BingleSeq puts the best and most widely used packages and tools for RNA-Seq analyses at the fingertips of biologists with no programming experience.