All published data are made available on either our FTP site or within individual publications or their locally-hosted supplements. Published microarray data are also available within the Princeton University MicroArray database (PUMAdb).
Yeast Functional Genomics database (YFGdb): ftp://gen-ftp.princeton.edu/yfgdb/
Princeton Protein Orthology Database (P-POD): ftp://gen-ftp.princeton.edu/ppod/
- ChARM: for detection of aneuploidies in array CGH and gene expression microarray data.
- FIRE: A universal framework for regulatory element discovery across all genomes and data-types.
- Nearest Neighbor Networks: graph-based algorithm used to cluster genes with similar microarray expression profiles.
- PUMAdb: Software underlying the microarray database.
- PVIEW: Software that enables quantification of complex mixtures of proteins and metabolites assayed by LC-MS and LC-MS/MS.
- Sleipnir Library for Computational Functional Genomics: Sleipnir is a C++ library enabling efficient analysis, integration, mining, and machine learning over genomic data. This includes a particular focus on microarrays, since they make up the bulk of available data for many organisms, but Sleipnir can also integrate a wide variety of other data types, from pairwise physical interactions to sequence similarity or shared transcription factor binding sites.
When feasible, algorithms and other software tools developed as part of the CQB are implemented for the web to provide convenient, widespread access to the entire research community. These are available from our Bioinformatics Tools and Resources page.