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.
| Version: | 0.2.7 |
| Depends: | R (≥ 3.6) |
| Imports: | dplyr, RCurl, fst, stringi, stringr |
| Suggests: | testthat (≥ 3.0.0) |
| Published: | 2022-11-20 |
| DOI: | 10.32614/CRAN.package.geneset |
| Author: | Yunze Liu  [aut,
cre] |
| Maintainer: | Yunze Liu <jieandze1314 at gmail.com> |
| BugReports: | https://github.com/GangLiLab/geneset/issues |
| License: | GPL-3 |
| URL: | https://github.com/GangLiLab/geneset |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | geneset results |
Documentation:
| Reference manual: | geneset.html , geneset.pdf |
Downloads:
| Package source: | geneset_0.2.7.tar.gz |
| Windows binaries: | r-devel: geneset_0.2.7.zip, r-release: geneset_0.2.7.zip, r-oldrel: geneset_0.2.7.zip |
| macOS binaries: | r-release (arm64): geneset_0.2.7.tgz, r-oldrel (arm64): geneset_0.2.7.tgz, r-release (x86_64): geneset_0.2.7.tgz, r-oldrel (x86_64): geneset_0.2.7.tgz |
| Old sources: | geneset archive |
Reverse dependencies:
| Reverse imports: | genekitr, MIRit |
Linking:
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