limma for differential gene expression analysis of microarray or RNA seq data, also includes functions for enrichment analysis
edgeR for differential gene expression analysis of RNA seq data
DESeq2 for differential gene expression analysis of RNA seq data
From reads to genes to pathways Pipeline for DGE analysis and pathway analysis
fgsea package with fgsea() function called by clusterProfiler
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.
bioconductor Introduction and structure
online tool for overrepresentation analysis
online tool for gene set enrichment analysis
Revigo and rrvgo
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.
For fungi, FungiDB provides identification of metabolic pathways based on list of genes
PlantGSAD: a gene set database for plants https://academic.oup.com/nar/article/50/D1/D1456/6371972?login=true
Eventually this repository by Zhang et al