Programs and bioinformatic odds and ends

These are Perl programs. Run them without parameters to see usage information.

Microarray-related

exp_list_mc

Calculates the probability a gene set shows average expression response different from a random group of genes sampled from the input dataset.

Comparative Genomic Analysis Tools (CGAT)

As part of my thesis project in Roger Reeves's lab at Johns Hopkins University, I developed a package of genomic DNA analysis tools, CGAT.

CGAT site 2.
 

You can download the current version, CGAT_0.910.tar.gz.

Software for weekly Pubmed searches

The software which performs the weekly PubMed biomedical literature searches is freely available under the GNU General Public License. This software is setup for GNU/Linux, but the Perl code isn't OS specific. A cron job runs a Perl program once a week that searches for new papers matching the search terms. Perl one-liners then add the weekly search results to three web pages.

get_pubmed. The Perl program which searches PubMed.
pubmed.lookup. Cron job which calls get_pubmed and the one-liners.


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Please send comments or questions regarding this web page to Jim Lund (jiml at uky dot edu)