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DEAGO generates user-friendly quality control (QC) and analysis reports for RNA-Seq datasets. These interactive reports can be opened simply in a web browser and provide a simple way of sharing information about your analysis with collaborators.
DEAGO uses a Perl wrapper module (Bio-Deago) to generate a HTML report from markdown templates by calling functions from an R package (deago).
There are three main steps to each analysis:
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Generating QC plots (ggplot2)
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Identifying differentially expressed (DE) genes (DESeq2)
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Performing gene ontology (GO) term enrichment analyses (topGO)
Before working with DEAGO, you will first need to have installed:
Note: For Sanger pathogens users, these are already available on pcs5 and farm3.
The DEAGO user guide can be found here.
There is a short DEAGO tutorial here which will give you an opportunity to look at example input data, run some DEAGO analyses and look at the output files which are generated.
We also have a separate Sanger pathogen users page for Sanger pathogen users which shows you how to prepare your input data from the Sanger pathogen pipelines.