Hi there! Thanks for using ARACNe-AP. To convert the ARACNe-AP into an R object, this is what we used to do. Assuming all the outputs of ARACNe-AP are saved as files 3col.gz Loading code: library(viper) library(mixtools) Necessary functions: aracne2regulon<-function(afile, eset) { dset <- eset annot <- rownames(eset) names(annot) <- rownames(eset) rm(eset) tmp <- as.matrix(read.delim(afile,as.is=TRUE,header=TRUE)[,1:3]) aracne <- data.frame(tf=tmp[, 1], target=tmp[, 2], mi=as.numeric(tmp[, 3])/max(as.numeric(tmp[,...
Hi Juan! This implementation of aracne is to be run directly as a jar file from the command line. E.g. java -jar Aracne.jar Try to run some of the examples in the wiki from the command line (from the Windows command prompt or the Ubuntu terminal, for example).
Hi Juan! Aracne-geWrokbench is not maintained by us, you should contact Aristidis Floratos at Columbia University for it. As an alternative, you can use our Aracne-AP, which doesn't require a microarray name to run!
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Cindy was fixed in the consolidation step
Working great before experimenting on the Poiss...
Updated Cindy executable to the fixed version
BUG FIX for data containing lots of identical v...
Now an ECLIPSE MARS project
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