[Bioc-devel] GOexpress: new package to visualise microarray and RNAseq data using gene ontology annotations

Kevin Rue-Albrecht kevin.rue at ucdconnect.ie
Tue Oct 7 13:24:55 CEST 2014

Dear all,

I would like to introduce a recent addition to Bioconductor.
I hope those of you working with transcriptomics data will find it useful
for their own work.

*GOexpress *is a package taking an *ExpressionSet *object minimally
including *assayData *and *phenoData* corresponding to either microarray or
RNA-Sequencing data, and enables rapid plotting of the expression profile
of any given gene in the different experimental groups. The package also
initially fetches gene ontology annotations from the *Ensembl BioMart* to
display the expression level of genes associated with each ontology in a
heatmap. Consequently, all species and microarray present in the *Ensembl
BioMart* should be supported by *GOexpress* (only a few were tested during
the development of the package).

We included two scoring methods (random-forest and ANOVA) to rank genes and
gene ontologies best clustering predefined groups of samples (e.g.
treatment groups). Note that we do not intend to compete with packages such
as GOstats and topGO for hypothesis testing, but rather to complement such
packages with means of accompanying their result statistics with plots
showing group-wise and sample-wise expression levels.

I have a few more ideas of my own to extend the package when time allows,
but I do also welcome feedback and suggestions from testers that could
benefit the community.

Link: http://bioconductor.org/packages/devel/bioc/html/GOexpress.html

Yours sincerely,

Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin

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