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.
- clustifyr: an R package for automated single-cell RNA sequencing cluster classificationF1000Res., 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.
- valr: Reproducible genome interval analysis in RF1000Res., Jun 2017