[Bioperl-l] Algorithm::Cluster for clustering gene expression data

[Michiel Jan Laurens de Hoon]

During 2002, our laboratory developed a library of C routines that 
implement various clustering methods commonly used to analyze gene 
expression data. These include hierarchical (pairwise single-, maximum-, 
centroid-, and average-linkage) clustering, k-means clustering, and 
self-organizing maps on a 2D rectangular topology. We generated this 
library with the use of scripting languages in mind.

Recently John Nolan of the University of California, Santa Cruz 
developed a Perl interface to the clustering library. Hoping that this 
module will be useful to the Perl and Bioperl community, we have made it 
available on CPAN and at 
http://bonsai.ims.u-tokyo.ac.jp/%7Emdehoon/software/cluster, where you 
can also find a manual.

To install, download Algorithm-Cluster-1.17.tar.gz, unpack, and 
run perl Makefile.PL; make; make test; make install as usual. (The 
version number is based on the underlying C library). The source 
distribution contains a test suite and a number of example Perl scripts. 
For users of ActiveState's Perl on Windows, use the Perl Package Manager 
ppm as in (on one line)
ppm install 
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/Algorithm-Cluster.ppd

One caveat: The module currently does not work on Cygwin. Cygwin's Perl 
seems to have problems understanding floating point values. No problems 
were detected on Windows with ActiveState's Perl, Mac OS X, Unix, and Linux.

This software was released under the GNU Lesser General Public License. 
Bug reports and suggestions for improvement (better yet, patches) are 
most welcome.

And thanks again, John.

Michiel de Hoon
University of Tokyo, Human Genome Center.

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon