Software development

We develop software packages and provide complete analysis workflows for our studies. The complete collection of software packages are available on the RBI Github page.

Our public data sets are available at the NCBI Gene Expression Omnibus.


raer facilitates analysis of RNA adenosine editing in the Bioconductor ecosystem, enabling rigorous identification of editing events from both bulk and single-cell mRNA sequencing experiments.


djvdj provides a range of tools to analyze and manipulate single cell V(D)J sequencing data, with a particular focus on a facile user experience, providing publication-quality plots exploring the VDJ repertoire and associated gene expression patterns.


clustifyr classifies cells and clusters in single-cell RNA sequencing experiments using reference bulk RNA-seq data sets, sorted microarray expression data, single-cell gene signatures, or lists of marker genes.

  1. clustifyr.png
    clustifyr: an R package for automated single-cell RNA sequencing cluster classification
    Rui Fu, Austin E Gillen, Ryan M Sheridan, Chengzhe Tian, Michelle Daya, Yue Hao, Jay R Hesselberth, and Kent A Riemondy
    F1000Res., Apr 2020


valr provides tools to read and manipulate genome intervals and signals, similar to the BEDtools suite. valr enables analysis in the R/RStudio environment, leveraging modern R tools in the tidyverse for a terse, expressive syntax.

  1. valr.png
    valr: Reproducible genome interval analysis in R
    Kent A Riemondy, Ryan M Sheridan, Austin Gillen, Yinni Yu, Christopher G Bennett, and Jay R Hesselberth
    F1000Res., Jun 2017