Software development

Software and analyis pipelines

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


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.


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.