November 21, 2007

Two new methods papers have come out. The first article describes the dynamic tree cut algorithm that is used to cut branches of a hierarchical cluster tree (Langfelder P, Zhang B, Horvath S 2007) LINK TO WEBPAGE. Different from the default method that uses the same cutting height for each branch, this algorithm automatically chooses a height cut-off by taking the cluster shape into account.
The second paper describes how to use module eigengenes to construct a network between modules (Langfelder Horvath 2007) LINK TO WEBPAGE.
 

March 24, 2008

We are releasing a user-friendly, menu driven stand-alone software (called WGCNA), which can be used to identify significant modules and pathways. The software does *not* require knowledge of R software commands but it requires that R be installed.
 

April 15, 2008

We have published an article on orienting (also known as directing) the edges of a quantitative trait or gene co-expression network if genetic marker data (SNPs) are available. See the reference Aten JE, Fuller TF, Lusis AJ, Horvath S (2008) Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Systems Biology 2008, 2:34 LINK TO PAPER. Accompanying R software can be found here LINK TO WEBPAGE