Software development

Software and analyis pipelines

We provide complete analysis workflows for our studies. The complete collection of software packages are available at:

Our public data sets are available:


djvdj provides a range of tools to analyze and manipulate single cell V(D)J sequencing data.


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.

Fu R, Gillen AE, Sheridan RM, Tian C, Daya M, Hao Y, Hesselberth JR, Riemondy KA. clustifyr: an R package for automated single-cell RNA sequencing cluster classification. F1000Res. 2020 Apr 1;9:223. PMCID: PMC7383722


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.

Riemondy KA, Sheridan RM, Gillen A, Yu Y, Bennett CG, Hesselberth JR. valr: Reproducible genome interval analysis in R. F1000Res. F1000 Research Ltd; 2017 Jun 29;6:1025. PMCID: PMC5506536