gogadget: an R package for go analysis visualization and interpretation
I have developed an R package, which can help in the interpretation and visualization of GO enrichment analysis. The strategy of this package is to first do goseq analysis for your RNA-seq data. Subsequently, gogadget offers functions to make sense out of these goseq results.
gogadget.p.adjust adds an adjusted p-value to the results.
gogadget.explore explores possible (ideal) filtering settings. The idea is to filter out GO terms that are too general or too specific.
gogadget.filter filters with the ideal settings (found with the previous function).
gogadget.heatmap groups the GO terms that are similar together. Similarity is based on overlapping genes between the terms.
Fifth and sixth functions,
gogadget.gmt, respectively, can export your filtered results to cytoscape EnrichmentMap.
The package is developed in R 3.3.2. on windows 7, and was also tested on Ubuntu 14.04. To install the package, download the tar.gz file from https://sourceforge.net/projects/gogadget/ and use the following code in R:
install.packages( "C:/your/directory/gogadget_2.0.tar.gz", repos = NULL, type="source")
I have written an extensive user's guide, which is also available on https://sourceforge.net/projects/gogadget/. Furthermore, there is a case study which you can try (files also on sourceForge).
Please cite the following paper if you publish results obtained using gogadget:
Nota, B. (2017), Gogadget: an R Package for Interpretation and Visualization of GO Enrichment Results. Mol. Inf. May;36(5-6). doi: 10.1002/minf.201600132
Let me know if there are questions or comments. Thank you.