Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.
Drier Y, Sheffer M, Domany E. Pathway-based personalized analysis of cancer. Proceedings of the National Academy of Sciences, 2013, vol. 110(16) pp:6388-6393. (www.pnas.org/cgi/doi/10.1073/pnas.1219651110)
See more information on : http://www.weizmann.ac.il/pathifier/
1 2 3 4 5
data(KEGG) # Two pathways of the KEGG database data(Sheffer) # The colorectal data of Sheffer et al. PDS<-quantify_pathways_deregulation(sheffer$data, sheffer$allgenes, kegg$gs, kegg$pathwaynames, sheffer$normals, attempts = 100, logfile="sheffer.kegg.log", min_exp=sheffer$minexp, min_std=sheffer$minstd)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.