The baerhunter package comprises a set of tools for the prediction, annotation and filtering of bacterial intergenic expressed regions from RNA-seq data. In addition, it supports further stages of bacterial RNA-seq data analysis, such as transcript abundance quantification and differential gene expression testing. It also offers additional options for the selection of genomic features by their expression strength and editing of the annotation file.
A. Ozuna, D. Liberto, R. M. Joyce, K.B. Arnvig, I. Nobeli. baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data. https://doi.org/10.1093/bioinformatics/btz643
J. Stiens, Y.Y. Tan, R. Joyce, K.B. Arnvig, S.L. Kendall, I. Nobeli. Using a Whole Genome Co-expression Network to Inform the Functional Characterisation of Predicted Genomic Elements from Mycobacterium tuberculosis Transcriptomic Data. https://onlinelibrary.wiley.com/doi/10.1111/mmi.15055