├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── 00_S4_generic_methods.R ├── 00_global.R ├── RcppExports.R ├── extend.R ├── get_data.R ├── great_client.R ├── great_local.R ├── ncbi.R ├── shiny.R ├── utils.R ├── volcano.R └── zzz.R ├── README.md ├── _pkgdown.yml ├── docs ├── 404.html ├── LICENSE-text.html ├── articles │ ├── 1.online-GREAT.html │ ├── 1.online-GREAT_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ └── unnamed-chunk-18-1.png │ ├── 2.local-GREAT.html │ ├── 2.local-GREAT_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ └── unnamed-chunk-18-1.png │ ├── 3.other-geneset-databases.html │ ├── 4.other-organisms.html │ ├── custom.css │ ├── group_associations.html │ ├── group_associations_files │ │ └── figure-html │ │ │ └── unnamed-chunk-2-1.png │ ├── index.html │ ├── local-GREAT.html │ ├── local-GREAT_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ └── unnamed-chunk-19-1.png │ ├── online-GREAT.html │ ├── online-GREAT_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ └── unnamed-chunk-18-1.png │ ├── other-docs.html │ ├── other-geneset-databases.html │ ├── other-organisms.html │ ├── rGREAT.html │ ├── rGREAT_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ └── unnamed-chunk-15-1.png │ ├── suppl_compare_GO.html │ ├── suppl_compare_GO_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ └── unnamed-chunk-7-1.png │ ├── suppl_compare_genome_versions.html │ ├── suppl_compare_genome_versions_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── suppl_compare_online_and_local.html │ ├── suppl_compare_online_and_local_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── suppl_compare_tss.html │ ├── suppl_compare_tss_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── suppl_use_background.html │ └── suppl_use_background_files │ │ └── figure-html │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-13-1.png │ │ ├── unnamed-chunk-14-1.png │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-6-1.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── GreatJob-class.html │ ├── GreatJob.html │ ├── GreatObject-class.html │ ├── GreatObject.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── availableCategories-GreatJob-method.html │ ├── availableOntologies-GreatJob-method.html │ ├── extendTSS.html │ ├── extendTSSFromDataFrame.html │ ├── extendTSSFromOrgDb.html │ ├── extendTSSFromTxDb.html │ ├── getEnrichmentTable-GreatJob-method.html │ ├── getEnrichmentTable-GreatObject-method.html │ ├── getEnrichmentTable-dispatch.html │ ├── getEnrichmentTables-GreatJob-method.html │ ├── getEnrichmentTables-GreatJob-method.rd │ ├── getEnrichmentTables-GreatObject-method.html │ ├── getEnrichmentTables-dispatch.html │ ├── getGREATDefaultTSS.html │ ├── getGapFromUCSC.html │ ├── getGencodeGenes.html │ ├── getGeneSetsFromBioMart.html │ ├── getGeneSetsFromOrgDb.html │ ├── getGenesFromGencode.html │ ├── getGenomeDataFromNCBI.html │ ├── getKEGGGenome.html │ ├── getKEGGPathways.html │ ├── getRefSeqGenesFromUCSC.html │ ├── getRegionGeneAssociations-GreatJob-method.html │ ├── getRegionGeneAssociations-GreatObject-method.html │ ├── getRegionGeneAssociations-dispatch.html │ ├── getTSS.html │ ├── great.html │ ├── great_opt.html │ ├── index.html │ ├── plotRegionGeneAssociationGraphs-GreatJob-method-1.png │ ├── plotRegionGeneAssociationGraphs-GreatJob-method-2.png │ ├── plotRegionGeneAssociationGraphs-GreatJob-method-3.png │ ├── plotRegionGeneAssociationGraphs-GreatJob-method.html │ ├── plotRegionGeneAssociations-GreatJob-method-1.png │ ├── plotRegionGeneAssociations-GreatJob-method-2.png │ ├── plotRegionGeneAssociations-GreatJob-method-3.png │ ├── plotRegionGeneAssociations-GreatJob-method.html │ ├── plotRegionGeneAssociations-GreatObject-method-1.png │ ├── plotRegionGeneAssociations-GreatObject-method.html │ ├── plotRegionGeneAssociations-dispatch.html │ ├── plotVolcano-GreatJob-method.html │ ├── plotVolcano-GreatObject-method.html │ ├── plotVolcano-dispatch.html │ ├── randomRegions.html │ ├── randomRegionsFromBioMartGenome.html │ ├── read_gmt.html │ ├── reduce_by_start_and_end.html │ ├── shinyReport-GreatJob-method.html │ ├── shinyReport-GreatObject-method.html │ ├── shinyReport-dispatch.html │ ├── submitGreatJob.html │ └── submitGreatJob.rd └── sitemap.xml ├── inst ├── CITATION └── extdata │ ├── CHR_LEN_DB.rds │ ├── GREATv4.genes.hg19.tsv.gz │ ├── GREATv4.genes.hg38.tsv.gz │ ├── GREATv4.genes.mm10.tsv.gz │ ├── GREATv4.genes.mm9.tsv.gz │ ├── GreatJob.rds │ ├── GreatObject.rds │ ├── bioc_anno_pkgs.csv │ ├── biomart_genesets.R │ ├── download_ncbi_genome_data.pl │ ├── gencode_gene.rds │ ├── msigdb_genesets.R │ ├── objects.R │ ├── parse_gencode.pl │ ├── tb_encTfChipPkENCFF215YWS_GM12878_MYB_hg19.bed.gz │ └── ucsc_gaps.rds ├── man ├── GreatJob-class.rd ├── GreatJob.rd ├── GreatObject-class.Rd ├── GreatObject.Rd ├── availableCategories-GreatJob-method.rd ├── availableOntologies-GreatJob-method.rd ├── extendTSS.Rd ├── extendTSSFromDataFrame.Rd ├── extendTSSFromOrgDb.Rd ├── extendTSSFromTxDb.Rd ├── getEnrichmentTable-GreatJob-method.Rd ├── getEnrichmentTable-GreatObject-method.Rd ├── getEnrichmentTable-dispatch.Rd ├── getEnrichmentTables-GreatJob-method.rd ├── getEnrichmentTables-GreatObject-method.Rd ├── getEnrichmentTables-dispatch.Rd ├── getGREATDefaultTSS.Rd ├── getGapFromUCSC.Rd ├── getGeneSetsFromBioMart.Rd ├── getGeneSetsFromOrgDb.Rd ├── getGenesFromGencode.Rd ├── getGenomeDataFromNCBI.Rd ├── getKEGGGenome.Rd ├── getKEGGPathways.Rd ├── getRefSeqGenesFromUCSC.Rd ├── getRegionGeneAssociations-GreatJob-method.Rd ├── getRegionGeneAssociations-GreatObject-method.Rd ├── getRegionGeneAssociations-dispatch.Rd ├── getTSS.Rd ├── great.Rd ├── great_opt.Rd ├── plotRegionGeneAssociationGraphs-GreatJob-method.rd ├── plotRegionGeneAssociations-GreatJob-method.Rd ├── plotRegionGeneAssociations-GreatObject-method.Rd ├── plotRegionGeneAssociations-dispatch.Rd ├── plotVolcano-GreatJob-method.Rd ├── plotVolcano-GreatObject-method.Rd ├── plotVolcano-dispatch.Rd ├── randomRegions.Rd ├── randomRegionsFromBioMartGenome.Rd ├── read_gmt.Rd ├── reduce_by_start_and_end.Rd ├── shinyReport-GreatJob-method.Rd ├── shinyReport-GreatObject-method.Rd ├── shinyReport-dispatch.Rd └── submitGreatJob.rd ├── src ├── RcppExports.cpp └── reduce_by_start_and_end.cpp ├── tests ├── test-all.R ├── test-no-run.R └── testthat │ ├── test_available.R │ └── test_great.R └── vignettes ├── data ├── A549_MYC_encTfChipPkENCFF542GMN_hg38.bed ├── GM12878_chromHMM.bed.gz ├── GREATv4.genes.hg19.tsv.gz 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