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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 |
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 |
Reference manual: | geneset.pdf |
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 imports: | genekitr, MIRit |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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