Software from the Hibbs Lab
SPELL is an online search engine for large compendia of gene expression microarray data. The current SPELL website is based on a collection of ~2400 S. cerevisiae microarray conditions. The underlying algorithm is a query-driven search utilizing a novel application of SVD for signal balancing and using the Fisher Z-transform for improved comparability between datasets.
Go to the SPELL search engine
- Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics, 2007
GOLEM is a tool for viewing, navigating, and analyzing the hierarchical structure and annotations to the gene ontology. The visualization component allows a user to see the local graph structure around a GO term of interest and navigate to nearby nodes. GOLEM also provides the ability to look for statistical enrichment of GO terms in lists of genes and then observe the relationships between those terms. GOLEM is available both as an applet for use online and as a standalone download.
- Sealfon RS G, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics, 2006
geneVAnD is an implementation of several visualization techniques that incorporate meaningful statistics that are noise-robust for the purpose of analyzing the results of clustering algorithms on microarray data. This includes a rank-based visualization method that is more robust to noise, a difference display method to aid assessments of cluster quality and detection of outliers, and a projection of high dimensional data into a three dimensional space in order to examine relationships between clusters. Our methods are interactive and are dynamically linked together for comprehensive analysis. Further, our approach applies to both protein and gene expression microarrays, and our architecture is scalable for use on both desktop/laptop screens and large-scale display devices.
- Hibbs MA, Dirksen NC, Li K, Troyanskaya OG. Visualization methods for statistical analysis of microarray clusters. BMC Bioinformatics, 2005
HIDRA is a visualization and analyis framework for simultaneously exploring multiple microarray datasets at once. HIDRA allows users to quicky identify patterns common across many datasets as well as patterns unique to individual datasets. HIDRA is currently in beta testing and is still under development.
- Hibbs MA, Wallace G, Dunham M, Li K, Troyanskaya OG. Viewing the Larger Context of Genomic Data through Horizontal Integration. 11th International Conference Information Visualization (IV07), 2007
- Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin A. Visualization of omics data for systems biology. Nature Methods, 2010
WCluster is a java program designed to perform hierarchical clustering. Whereas most hierarchical clustering software only allows users to assign weights to either rows or columns, WCluster lets you assign weights to individual data points. For example, this can be very useful if a particular row should be down-weighted under only a subset of the columns.