COHCAP is now available in Bioconductor!

[Charles Warden]

COHCAP is now available as a Bioconductor package in R:

http://www.bioconductor.org/packages/devel/bioc/html/COHCAP.html

This may be preferable to the stand alone version for users that are familiar with R. The Bioconductor version does not require Java to be installed nor does it require users to specify the location of an Rscript executable file. Bioconductor is a popular resource for distributing many important bioinformatics tools.

The input and output files are slightly different, but functionality is essentially the same for both the standalone and Bioconductor versions of COHCAP.

The Bioconductor package will not provide a GUI for basic users without coding experience. Users uncomfortable with using R should use the standalone version of COHCAP that can be downloaded from this website.

There is a detailed protocol for analysis of 450k Data on Protocol Exchange: http://www.nature.com/protocolexchange/protocols/2965

Issues with the Bioconductor package should be listed as “Bioconductor: [issue description]”

FYI, the Bioconductor package is currently a 'devel' version due to the Bioconductor release schedule. This means that you will need to use R-devel in order to install the package via biocLite(). Once the new version of Bioconductor is released, this post will be updated accordingly. Until that time, here is the link for install R-devel on a Windows machine:

http://cran.r-project.org/bin/windows/base/rdevel.html

[Charles Warden]

COHCAP is now available as a release package:

http://bioconductor.org/packages/release/bioc/html/COHCAP.html

So, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).