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perseus:user:activities:matrixprocessing:wgcna [2018/07/17 17:41]
rudolph created
perseus:user:activities:matrixprocessing:wgcna [2018/07/17 18:24] (current)
rudolph
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 ====== WGCNA ====== ====== WGCNA ======
 +Weighted Gene Co-expression Network Analysis
  
 +This package is provided through the R-language integration into Perseus and therefore requires R as well as the package itself to be installed in order to be used. Visit the [[https://​github.com/​jdrudolph/​PluginInterop|PluginInterop]] and [[https://​github.com/​jdrudolph/​PerseusR|PerseusR]] for additional technical information on the integration of R and Perseus.
 +
 +==== Installation ====
   * Download the R installer install it.   * Download the R installer install it.
   * Remember the R installation directory. If you do not know where you have installed R, check the default location ''​C:​\Program Files\R\R-3.5.0\bin'',​ or search for ''​Rscript.exe''​.   * Remember the R installation directory. If you do not know where you have installed R, check the default location ''​C:​\Program Files\R\R-3.5.0\bin'',​ or search for ''​Rscript.exe''​.
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 library(devtools) library(devtools)
 install_github('​jdrudolph/​PerseusR'​) </​code>​ install_github('​jdrudolph/​PerseusR'​) </​code>​
 +  * You should now be able to load the WGCNA and PerseusR libraries by entering the following code. Upon loading, WGCNA will print some output, while PerseusR will not print any. <​code>​
 +library(WGCNA)
 +library(PerseusR) </​code>​
 +You are now ready to perform co-expression analysis from within Perseus.
 +
 +==== WGCNA functions ====
 +  * [[perseus:​user:​activities:​matrixprocessing:​wgcna:​soft-threshold|Soft-threshold]]
 +  * [[perseus:​user:​activities:​matrixanalysis:​clustering_pca:​co-expression_clustering|Co-expression clustering]]
perseus/user/activities/matrixprocessing/wgcna.txt ยท Last modified: 2018/07/17 18:24 by rudolph