RLSuite: An integrative R-loop bioinformatics framework

Abstract

R-loops are three-stranded nucleic acid structures containing RNA:DNA hybrids. While R-loop mapping via high-throughput sequencing can reveal novel insight into R-loop biology, the analysis and quality control of these data is a non-trivial task for which few bioinformatic tools exist. Herein we describe RLSuite, an integrative R-loop bioinformatics framework for pre-processing, quality control, and downstream analysis of R-loop mapping data. RLSuite enables users to compare their data to hundreds of public datasets and generate a user-friendly analysis report for sharing with non-bioinformatician colleagues. Taken together, RLSuite is a novel analysis framework that should greatly benefit the emerging R-loop bioinformatics community.

Approaches for Mapping and Analysis of R‐loops

“…To address current limitations, we recently described RLSuite, a collection of software packages that provide an integrative R‐loop bioinformatics framework (Miller, Montemayor, Levy, et al., 2023). The core components of RLSuite are (1) RLPipes, a CLI utility for automated upstream processing of R‐loop mapping datasets; (2) RLHub an R/Bioconductor package for accessing processed R‐loop mapping data; and (3) RLSeq a feature‐rich R/Bioconductor package for the downstream analysis of R‐loop mapping data.…”