geneset

Gene sets are fundamental for gene enrichment analysis. The package 'geneset' enables querying gene sets from public databases including 'GO' (Gene Ontology Consortium. (2004) doi:10.1093/nar/gkh036), 'KEGG' (Minoru et al. (2000) doi:10.1093/nar/28.1.27), 'WikiPathway' (Marvin et al. (2020) doi:10.1093/nar/gkaa1024), 'MsigDb' (Arthur et al. (2015) doi:10.1016/j.cels.2015.12.004), 'Reactome' (David et al. (2011) doi:10.1093/nar/gkq1018), 'MeSH' (Ish et al. (2014) doi:10.4103/0019-5413.139827), 'DisGeNET' (Janet et al. (2017) doi:10.1093/nar/gkw943), 'Disease Ontology' (Lynn et al. (2011) doi:10.1093/nar/gkr972), 'Network of Cancer Genes' (Dimitra et al. (2019) doi:10.1186/s13059-018-1612-0) and 'COVID-19' (Maxim et al. (2020) doi:10.21203/rs.3.rs-28582/v1). Gene sets are stored in the list object which provides data frame of 'geneset' and 'geneset_name'. The 'geneset' has two columns of term ID and gene ID. The 'geneset_name' has two columns of terms ID and term description.