Software

CGHweb (http://compbio.med.harvard.edu/CGHweb)

This tool provides an interface to apply several popular algorithms to segment a copy-number profile from CGH (comparative genomic hybridization) data. It generates a heatmap panel of the segmented profiles for each method as well as a consensus profile. The clickable heatmap can be moved along the chromosome and zoomed in or out. It also displays the time that each algorithm took and provides numerical values of the segmented profiles for download.

nuScore (http://compbio.med.harvard.edu/nuScore)

This allows estimation of the affinity of the histone core to DNA and prediction of nucleosome arrangement on a given sequence. The algorithm is based on assessment of the energy cost of imposing the deformations required to wrap DNA around the histone surface

ChIP-chip normalization

An R package will be available in May, 2008

CrossChip (http://www.crosschip.org)

This tool is for integrating data from multiple generations of Affymetrix GeneChips. Matching probes based on Affymetrix "best-match" is inadequate for most analyses. This tool allows the user to derive a list of similar probes based on the user-specified criteria on probe sequence similarity and the minimum number of probe pairs needed for each probe set.

sigPathway (for finding significant pathways from microarray data)

For the R package, please see the Supplementary Material page for the Tian et al article (Proc Natl Acad Sci, 2005). A web interface will be available shortly.