CNAmet is an algorithm and R package that facilitates the integration of copy number, methylation and expression data. In addition to the CNAmet algorithm, our R package includes the S2N algorithm for the integration of copy number to expression data. The CNAmet algorithm is also implemented as a component in the Anduril bioinformatics framework. Outputs of our algorithm include scores for methylation alteration induced expression, copy number aberration induced expression, a score for their combined effect, and adjacent p-values, which are also multiple hypothesis corrected.
News
Version 1.2 of CNAmet is now available. (16 May 2012)- We have updated the results for all of the available breast, ovarian and colorectal data from the Cancer Genome Atlas. We already have CNAmet results for ovarian online and will shortly have for breast and colorectal cancer. (10 April 2012)
- A hardware failure on July 26th caused our websites to go offline for three days. All services have since been restored. (27 July 2011)
Download
There are three versions of the R package.
- CNAmet_1.2_32bit.tar.gz for 32bit Unix
- CNAmet_1.2_64bit.tar.gz for 64bit Unix
- CNAmet_1.1.zip for Windows
Citation
Louhimo, R. and Hautaniemi, S. CNAmet: an R package for integration of copy number, expression and methylation data Bioinformatics (2011) 27(6):887-888.
Miscellany
The source code of the case study written in Anduril script can be found here.
The article contains two case study - one with glioblastoma multiforme (GBM) and the other with ovarian cancer (OV) data. Both belong to larger analyses. The complete GBM data analysis can found as a part of the Anduril framework casestudy which is frequently updated. The ovarian cancer analysis results can be found here.
We invite you to browse and use these results freely, and we request you to cite either the Anduril (for GBM) or CNAmet article (for OV) in such cases.
Related websites
- TCGA glioblastoma analysis including CNAmet results
- TCGA ovarian cancer analysis including CNAmet results
- TCGA invasive breast carcinoma analysis (CNAmet results coming soon)
- TCGA colorectal carcinoma analysis (CNAmet results coming soon)
- Anduril bioinformatics framework
- API for the Anduril component that uses CNAmet
- Moksiskaan pathway integration tool for Anduril