We develop tools for bioinformatics research, including Web sites, desktop tools, and databases. Most of our software is open source. To see what we’re working on, visit our publicly-accessible repositories on BitBucket.org.
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.
- Download IGB from Bioviz.org
- Get the IGB source code from BitBucket
- Read the IGB User’s Guide
- Visit Loraine Lab Jira to see our current code sprint
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.
- Visit CressExpress Classic
- Visit CressExpress 2.0 – prototype
- Read the CressExpress paper in Plant Physiology
- Read the CressExpress Methods in Molecular Biology paper
ArabiTag is a Web site that reports EST support for alternative splicing events. The ArabiTag Web site reports. Use ArabiTag to identify EST libraries and sample types where splice variants are expressed.
ArabiTag was developed by Adam English, now at Baylor University, who also wrote PBJelly.