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, Kevin -- Kévin RUE-ALBRECHT Wellcome Trust Computational Infection Biology PhD Programme University College Dublin Ireland http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel