Useful links

limma for differential gene expression analysis of microarray or RNA seq data, also includes functions for enrichment analysis

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

edgeR for differential gene expression analysis of RNA seq data

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

DESeq2 for differential gene expression analysis of RNA seq data

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 bioconductor package, to visualise Gene Ontology (GO) enrichment analysis results on gene lists arising from different analyses such clustering or PCA. The significant GO categories are visualised as word clouds that can be combined with different plots summarising the underlying data.

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.

A recent publication (2020) on gene set analysis challenges, opportunities and future research.

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