R package for generating HTML reports from differential expression analyis and GO term enrichment.
Generation of user-friendly HTML reports from differential expression analyis (DESeq2) and GO term enrichment (topGO) of count data using knitr. User provides count data and 'deago' will run the analysis and generate a HTML summary report containing QC plots, DE genes and top 30 GO terms.
deago has the following dependencies:
- R >= 3.2
- devtools
- DESeq2
- topGO
If you encounter an issue when installing deago please contact your local system administrator. If you encounter a bug please log it here or email us at path-help@sanger.ac.uk.
Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("sanger-pathogens/deago")
The test can be run from the top level directory, replacing <version> with the downloaded version:
R CMD build --no-build-vignettes .
R CMD check deago_<version>.tar.gz --no-vignettes --as-cran --no-manual
deago is free software, licensed under GPLv3.
Please report any issues to the issues page or email path-help@sanger.ac.uk.
If you use this software please cite:
DESeq2:
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M.I., Huber, W., Anders, S., Genome Biology 2014, 15:550. 10.1186/s13059-014-0550-8
topGO:
topGO: Enrichment Analysis for Gene Ontology
Alexa, A. and Rahnenfuhrer, J., 2016, r BiocStyle::pkg_ver('topGO')