genekitr - Gene Analysis Toolkit

Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inputting feature IDs. Enables easy retrieval of feature information, conversion of ID types, gene enrichment analysis, publication-level figures, group interaction plotting, and result export in one Excel file for seamless sharing and communication.

Last updated 2 months ago

enrichment-analysisgeneid-converterplotting

5.66 score 53 stars 1 packages 19 scripts 738 downloads

geneset - Get Gene Sets for Gene Enrichment Analysis

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.

Last updated 1 years ago

enrichment-analysisgenegeneset-enrichment

4.62 score 7 stars 2 packages 20 scripts 391 downloads