The avalanche of publications mentioning GO

November 30, 2010 | R on Guangchuang Yu

Gene Ontology is the de facto standard for annotation of gene products. It has been widely used in biological data mining, and I believe it will play more central role in the future. Publications mentioning GO was collected and deposited in GO ftp, and can be accessed (ftp://ftp.geneontology.... [Read more...]

The S3 OOP system

October 15, 2010 | R on Guangchuang Yu

R currently supports two internal OOP systems (S3 and S4), and several others as add-on packages, such as R.oo, and OOP. S3 is easy to use but not reliable enough for large software projects. The emphasis of the S3 system was on generic functions and polymorphism. It’s a ... [Read more...]


October 12, 2010 | R on Guangchuang Yu

It is very common to cluster genes based on their expression profiles, and also very common to integrate Gene Ontology to observe the distribution of biological processes, molecular functions and cellular components for a given gene list. But, what if the two in combination? The Gene Ontology distributions across a ... [Read more...]

highlight R syntax in wordpress using wp-codebox

October 10, 2010 | R on Guangchuang Yu

Tal Galili’s blog post mentioned that WP-Syntax can highlight R codes. I downloaded the modified version of WP-Syntax in his blog site. The plugin throw an error when activated. I did not try the original version hosted in Wordpress. I found that WP-CodeBox use GeShi for syntax highlighting as ... [Read more...]
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