CircSeqAlignTk

End-to-End Analysis of Small RNA-Seq Data from Viroids

CircSeqAlignTk is an end-to-end toolkit for RNA-Seq data analysis of circular genome sequences, supporting tasks from alignment to visualization. It is primarily designed for studying viroids, which are small, circular RNAs typically composed of a few hundred nucleotides. In addition to analysis capabilities, CircSeqAlignTk provides a streamlined interface for generating synthetic RNA-Seq data that closely mimics real datasets. This functionality enables developers to benchmark alignment tools, test novel alignment algorithms, and validate new workflows.

Installation

To install the CircSeqAlignTk package, start R (≥ 4.2) and run the following steps:

if (!requireNamespace('BiocManager', quietly = TRUE))
    install.packages('BiocManager')

BiocManager::install('CircSeqAlignTk')

Note that to install the latest version of the CircSeqAlignTk package, the latest version of R is required.

Documentation

Vignette, including overview of CircSeqAlignTk package, detailed explanation of functions, and several case studies, can be accessed with the following code.

browseVignettes('CircSeqAlignTk')

Citation

Sun J, Fu X and Cao W. CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes. F1000Research 2024, 11:1221. doi: 10.12688/f1000research.127348.2.