Package: rGREAT
Type: Package
Title: GREAT Analysis - Functional Enrichment on Genomic Regions
Version: 2.12.1
Date: 2025-11-05
Authors@R: person("Zuguang", "Gu", email = "z.gu@dkfz.de", role = c("aut", "cre"),
                  comment = c('ORCID'="0000-0002-7395-8709"))
Depends: R (>= 4.0.0), GenomicRanges, IRanges, methods
Imports: graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats,
        GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db,
        progress, circlize, AnnotationDbi,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer,
        S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp
Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager,
        org.Mm.eg.db, msigdbr, KEGGREST, reactome.db
Enhances: BioMartGOGeneSets, UniProtKeywords
VignetteBuilder: knitr
biocViews: GeneSetEnrichment, GO, Pathways, Software, Sequencing,
        WholeGenome, GenomeAnnotation, Coverage
Description: GREAT (Genomic Regions Enrichment of Annotations Tool) is
        a type of functional enrichment analysis directly performed on
        genomic regions. This package implements the GREAT algorithm
        (the local GREAT analysis), also it supports directly
        interacting with the GREAT web service (the online GREAT
        analysis). Both analysis can be viewed by a Shiny application.
        rGREAT by default supports more than 600 organisms and a large
        number of gene set collections, as well as self-provided gene
        sets and organisms from users. Additionally, it implements a
        general method for dealing with background regions.
URL: https://github.com/jokergoo/rGREAT,
        http://great.stanford.edu/public/html/
License: MIT + file LICENSE
LinkingTo: Rcpp
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev perl zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-05 10:02:16 UTC
RemoteUrl: https://github.com/bioc/rGREAT
RemoteRef: RELEASE_3_22
RemoteSha: 274c72de496f1f3460c7ad870b72a723c68b60c9
NeedsCompilation: yes
Packaged: 2025-11-11 17:05:59 UTC; root
Author: Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>)
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 17:15:22 UTC; windows
Archs: x64
