If you came here looking for the cMonkey R package, you're at the right place.

Note this R package is now superceded by a new python version of cMonkey, called cMonkey₂.

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To install (in R):

install.packages('devtools', dep=T)
require(devtools)
install_github('djreiss/cMonkey/cMonkey')

To install the data (or bigdata) packages:

install_github('djreiss/cMonkey/cMonkey.data')
install_github('djreiss/cMonkey/cMonkey.bigdata')

... and then go here

http://djreiss.github.io/cMonkey

for some additional documentation.

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If you want to run cMonkey from raw R scripts, you've come to the right place. All of the R files that are directly part of the cMonkey package are in the Rcode directory. (Note this code has been preprocessed to remove all of my testing and experimental functions.) The original files that contain my un-pre-processed, experimental code is in the ORIGINAL directory.

So, you can run cMonkey locally (without the package), after doing the following (in R):

for ( f in list.files( "Rcode", full=T ) ) source( f, chdir=T )

## And This is only necessary if you don't have the 'progs/' dir in your current dir (and will only work if
##     you have previously installed the cMonkey package):
progs.dir <- sprintf( "%s/progs/", system.file( package="cMonkey" ) )

cmonkey( ... ) ## run as you would if you had loaded the cMonkey package

## or:

e <- cMonkey.init(...); cmonkey( e, ..., dont.init=T )

## will work as well.

Visit http://djreiss.github.io/cMonkey for more instructions on using the package for your organism.