I was wondering if anyone could give some insight into the pathway analysis tools available in R. I would like to run an a pathway analysis to check for significantly enriched pathways using a genelist as the input. I did come across a gene2pathway package that is no longer supported and also a sigPathway tool but this is only available in the dev version of R.
I have read the post about tools to identify significantly altered pathways but it's been almost 10months and I would really appreciate any additional suggestions.
I like g:Profiler and the g:GOSt tool, which performs statistical enrichment analysis to provide interpretation of gene lists, using gene ontology terms, biological pathways, regulatory motifs of transcription factors and microRNAs, human disease annotations and protein-protein interactions. I use it via web interface on an occasional basis. I have just noticed that there is an R package available.