how about directly estimating the correlation matrix via shrinkage (e.g.
http://cran.r-project.org/web/packages/corpcor/index.html ) followed by
hierarchical clustering?  The direct estimate of [anti]correlation is given
by the former (i.e., the negative entries in the estimated correlation
matrix after shrinkage); if you want to proceed with clustering, you can do
the latter.

Other approaches exist that are better for specific problems, but taken at
face value, this would seem like the most straightforward for yours as
stated.



*He that would live in peace and at ease, *
*Must not speak all he knows, nor judge all he sees.*
*
*
Benjamin Franklin, Poor Richard's
Almanack<http://archive.org/details/poorrichardsalma00franrich>


On Fri, Nov 1, 2013 at 7:52 AM, Parth Patel <parth1415@gmail.com> wrote:

> Hi all,
>
>
>
> I have list of 1000 genes, and I am trying to perform anti-correlated
> clustering using R. Basically, I am trying to find genes that are
> anti-correlated out of 1000.
>
> Can you tell me what type of package should I use for doing anti-correlated
> clustering?
>
>
>
> Thanks in advance,
>
> Parth.
>
>
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