Useful links

limma for differential gene expression analysis, also includes functions for enrichment analysis

https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf

edgeR

https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

DESeq2

http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

From reads to genes to pathways Pipeline for DGE analysis and pathway analysis

https://f1000research.com/articles/5-1438

clusterProfiler e-Book

https://yulab-smu.github.io/clusterProfiler-book/

fgsea package with fgsea() function called by clusterProfiler

https://bioconductor.org/packages/release/bioc/html/fgsea.html

GOsummaries

https://www.bioconductor.org/packages/release/bioc/html/GOsummaries.html

bioconductor Introduction and structure

https://ivanek.github.io/analysisOfGenomicsDataWithR/02_IntroToBioc_html.html

online tool for overrepresentation analysis

http://www.pantherdb.org/

online tool for gene set enrichment analysis

http://www.webgestalt.org/

Revigo and rrvgo

http://revigo.irb.hr/

http://bioconductor.org/packages/release/bioc/html/rrvgo.html

A recent publication of the Gene Ontology consortium. They try to improve taxon constraints, i.e. to better define which terms are relevant for some species but not for others (such as leukocyte-related terms that should be constrained to vertebrates.

Tools for species other than human or mouse. Bioconductor contains “org.db” packages with genome/gene annotation for many organisms, for example for Drosophila or Arabidopsis.

For fungi, FungiDB provides identification of metabolic pathways based on list of genes

Eventually this repository by Zhang et al