Softwares‎ > ‎

netClass

netClass is an R packages for feature (gene) selection, which employ the biological network information to microarray classification.
(you can download from http://cran.r-project.org/web/packages/netClass/)

netClass implemented following methods:
average gene expression of pathway (aep), Guo et al., Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics 2005, 6:58.
pathway activitive classification (PAC), Lee E, Chuang H-Y, Kim J-W, Ideker T, Lee D (2008) Inferring Pathway Activity toward Precise Disease Classification. PLoS Comput Biol 4(11): e1000217.
Hub network Classsifccation, Taylor et al.(2009)Dynamic modularity in protein interaction networks predicts breast cancer outcome, Nat. Biotech.: doi: 10.1038/nbt.152
filter via top ranked genes(FrSVM), Yupeng Cun, Holger Fröhlich (2012) Integrating Prior Knowledge Into Prognostic Biomarker Discovery Based on Network Structure.arXiv:1212.3214 Winter C, Kristiansen G, Kersting S, Roy J, Aust D, et al. (2012) Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes. PLoS Comput Biol 8(5): e1002511. 
smoothed t-statistic(stSVM) , Yupeng Cun, Holger Fröhlich (2013) Data Integration via Network Smoothed T-Statistics.

for two classes microarry classification which employed the prior information.



ċ
netClass_1.2.tar.gz
(1532k)
CUN Y.,
Sep 17, 2013, 8:11 AM