Software

We have developed many open source tools for bioinformatics research, including Web sites, desktop tools, and code repositories for data analysis. To see what we’re working on, visit our publicly-accessible repositories on BitBucket.org.


LogoSphereIntegrated Genome Browser (IGB)

IGB is visualization software for genomics. Originally developed at Affymetrix to support fast visual exploration and analysis of tiling array data, we updated IGB to handle visualization of RNA-Seq, ChIP-Seq and other *seq data sets. IGB is free, open source software.


CressExpressCressExpress

CressExpress helps researchers identify functions for genes based on their expression patterns. Unlike all other tools, which pre-compute expression networks using all available data, CressExpress lets users select subsets of the data to include in an experiment. This is especially useful when working with genes with limited expression patterns. This allows detection of cell- or condition-specific transcriptional networks.

We released new version of CressExpress (version 2.0).


ArabiTagArabiTag – alternative splicing in Arabidopsis

ArabiTag is a Web site that reports EST support for alternative splicing events.

We published this site alongside a paper that assessed prevalence of alternative splicing in Arabidopsis.

ArabiTag was developed by Adam English, now at Baylor University, who also wrote PBJelly.