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Showing posts from March, 2017

GSEA in Bioconductor

Gene Set Enrichment Analysis is a test thought to find if the position of a group along a list implies some difference. The most know method is the one maintained by the Broad Institute . As it was the first widely used in biology and holds several collection of gene sets. A gene set is a collection of genes related, by either a function or an experiment, it is as fuzzy described as a pathway. In Bioconductor there is the under used tool of BiocViews , a topic for package classificacion. We can find a category for GSEAs under Software>BiologicalQuestion>GeneSetEnrichment . This category list 74 packages at the time of writing, which provide function for Gene Set Enrichment Analysis. It will be too long (and too hard for me) to describe all the packages in that category. However, it doesn't include all the packages that perform gene set enrichment. The first package for GSEA in Bioconductor one should look is GSEABase which provides with tools for reading files from

BioCor: My first package in Bioconductor

Yesterday I received an amazing email: Congratulations, BioCor has been added to Bioconductor! Yes, I had submitted a package for the Bioconductor project at the beginning of the week. The package calculates similarities between pathways, genes and clusters of genes based on their pathways. A pathway is a group of functionally related proteins, thus this similarities calculates the functional similarity of the pathway or genes in question. If anyone is curious what the email had this was in the body (I didn't know what to expect when I knew that it would be accepted):  Hi Lluís, Congratulations, BioCor has been added to Bioconductor! Currently, the definitive location for your Bioconductor package is in our SVN repository. The following information is to help you in your role as a package maintainer. You’ll need the following credentials to maintain your package: Subversion user ID: myuser Password: mypassword Package ‘landing pages’ Every package in Bi