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
Author: Yunze Liu ORCID iD [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.pdf

Downloads:

Package source: geneset_0.2.7.tar.gz
Windows binaries: r-devel: geneset_0.2.7.zip, r-release: not available, 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

Linking:

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