Files in jokergoo/rGREAT
GREAT Analysis - Functional Enrichment on Genomic Regions
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/00_S4_generic_methods.R
R/00_global.R
R/RcppExports.R
R/extend.R
R/get_data.R
R/great_client.R
R/great_local.R
R/ncbi.R
R/shiny.R
R/utils.R
R/volcano.R
R/zzz.R
README.md
_pkgdown.yml
build_pkg_site.R
docs/404.html
docs/LICENSE-text.html
docs/articles/1.online-GREAT.html
docs/articles/1.online-GREAT_files/figure-html/unnamed-chunk-14-1.png
docs/articles/1.online-GREAT_files/figure-html/unnamed-chunk-15-1.png
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docs/articles/2.local-GREAT.html
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docs/articles/3.other-geneset-databases.html
docs/articles/4.other-organisms.html
docs/articles/custom.css
docs/articles/group_associations.html
docs/articles/group_associations_files/figure-html/unnamed-chunk-2-1.png
docs/articles/index.html
docs/articles/local-GREAT.html
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docs/articles/other-docs.html
docs/articles/other-geneset-databases.html
docs/articles/other-organisms.html
docs/articles/rGREAT.html
docs/articles/rGREAT_files/figure-html/unnamed-chunk-12-1.png
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docs/articles/suppl_compare_GO.html
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docs/articles/suppl_compare_genome_versions.html
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docs/articles/suppl_compare_online_and_local.html
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docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/GreatJob-class.html
docs/reference/GreatJob.html
docs/reference/GreatObject-class.html
docs/reference/GreatObject.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/availableCategories-GreatJob-method.html
docs/reference/availableOntologies-GreatJob-method.html
docs/reference/extendTSS.html
docs/reference/extendTSSFromDataFrame.html
docs/reference/extendTSSFromOrgDb.html
docs/reference/extendTSSFromTxDb.html
docs/reference/getEnrichmentTable-GreatJob-method.html
docs/reference/getEnrichmentTable-GreatObject-method.html
docs/reference/getEnrichmentTable-dispatch.html
docs/reference/getEnrichmentTables-GreatJob-method.html
docs/reference/getEnrichmentTables-GreatJob-method.rd
docs/reference/getEnrichmentTables-GreatObject-method.html
docs/reference/getEnrichmentTables-dispatch.html
docs/reference/getGREATDefaultTSS.html
docs/reference/getGapFromUCSC.html
docs/reference/getGencodeGenes.html
docs/reference/getGeneSetsFromBioMart.html
docs/reference/getGeneSetsFromOrgDb.html
docs/reference/getGenesFromGencode.html
docs/reference/getGenomeDataFromNCBI.html
docs/reference/getKEGGGenome.html
docs/reference/getKEGGPathways.html
docs/reference/getRefSeqGenesFromUCSC.html
docs/reference/getRegionGeneAssociations-GreatJob-method.html
docs/reference/getRegionGeneAssociations-GreatObject-method.html
docs/reference/getRegionGeneAssociations-dispatch.html
docs/reference/getTSS.html
docs/reference/great.html
docs/reference/great_opt.html
docs/reference/index.html
docs/reference/plotRegionGeneAssociationGraphs-GreatJob-method-1.png
docs/reference/plotRegionGeneAssociationGraphs-GreatJob-method-2.png
docs/reference/plotRegionGeneAssociationGraphs-GreatJob-method-3.png
docs/reference/plotRegionGeneAssociationGraphs-GreatJob-method.html
docs/reference/plotRegionGeneAssociations-GreatJob-method-1.png
docs/reference/plotRegionGeneAssociations-GreatJob-method-2.png
docs/reference/plotRegionGeneAssociations-GreatJob-method-3.png
docs/reference/plotRegionGeneAssociations-GreatJob-method.html
docs/reference/plotRegionGeneAssociations-GreatObject-method-1.png
docs/reference/plotRegionGeneAssociations-GreatObject-method.html
docs/reference/plotRegionGeneAssociations-dispatch.html
docs/reference/plotVolcano-GreatJob-method.html
docs/reference/plotVolcano-GreatObject-method.html
docs/reference/plotVolcano-dispatch.html
docs/reference/randomRegions.html
docs/reference/randomRegionsFromBioMartGenome.html
docs/reference/read_gmt.html
docs/reference/reduce_by_start_and_end.html
docs/reference/shinyReport-GreatJob-method.html
docs/reference/shinyReport-GreatObject-method.html
docs/reference/shinyReport-dispatch.html
docs/reference/submitGreatJob.html
docs/reference/submitGreatJob.rd
docs/sitemap.xml
inst/CITATION
inst/extdata/CHR_LEN_DB.rds
inst/extdata/GREATv4.genes.hg19.tsv.gz
inst/extdata/GREATv4.genes.hg38.tsv.gz
inst/extdata/GREATv4.genes.mm10.tsv.gz
inst/extdata/GREATv4.genes.mm9.tsv.gz
inst/extdata/GreatJob.rds
inst/extdata/GreatObject.rds
inst/extdata/bioc_anno_pkgs.csv
inst/extdata/biomart_genesets.R
inst/extdata/download_ncbi_genome_data.pl
inst/extdata/gencode_gene.rds
inst/extdata/msigdb_genesets.R
inst/extdata/objects.R
inst/extdata/parse_gencode.pl
inst/extdata/tb_encTfChipPkENCFF215YWS_GM12878_MYB_hg19.bed.gz
inst/extdata/ucsc_gaps.rds
man/GreatJob-class.rd
man/GreatJob.rd
man/GreatObject-class.Rd
man/GreatObject.Rd
man/availableCategories-GreatJob-method.rd
man/availableOntologies-GreatJob-method.rd
man/extendTSS.Rd
man/extendTSSFromDataFrame.Rd
man/extendTSSFromOrgDb.Rd
man/extendTSSFromTxDb.Rd
man/getEnrichmentTable-GreatJob-method.Rd
man/getEnrichmentTable-GreatObject-method.Rd
man/getEnrichmentTable-dispatch.Rd
man/getEnrichmentTables-GreatJob-method.rd
man/getEnrichmentTables-GreatObject-method.Rd
man/getEnrichmentTables-dispatch.Rd
man/getGREATDefaultTSS.Rd
man/getGapFromUCSC.Rd
man/getGeneSetsFromBioMart.Rd
man/getGeneSetsFromOrgDb.Rd
man/getGenesFromGencode.Rd
man/getGenomeDataFromNCBI.Rd
man/getKEGGGenome.Rd
man/getKEGGPathways.Rd
man/getRefSeqGenesFromUCSC.Rd
man/getRegionGeneAssociations-GreatJob-method.Rd
man/getRegionGeneAssociations-GreatObject-method.Rd
man/getRegionGeneAssociations-dispatch.Rd
man/getTSS.Rd
man/great.Rd
man/great_opt.Rd
man/plotRegionGeneAssociationGraphs-GreatJob-method.rd
man/plotRegionGeneAssociations-GreatJob-method.Rd
man/plotRegionGeneAssociations-GreatObject-method.Rd
man/plotRegionGeneAssociations-dispatch.Rd
man/plotVolcano-GreatJob-method.Rd
man/plotVolcano-GreatObject-method.Rd
man/plotVolcano-dispatch.Rd
man/randomRegions.Rd
man/randomRegionsFromBioMartGenome.Rd
man/read_gmt.Rd
man/reduce_by_start_and_end.Rd
man/shinyReport-GreatJob-method.Rd
man/shinyReport-GreatObject-method.Rd
man/shinyReport-dispatch.Rd
man/submitGreatJob.rd
src/RcppExports.cpp
src/reduce_by_start_and_end.cpp
tests/test-all.R
tests/test-no-run.R
tests/testthat/test_available.R
tests/testthat/test_great.R
vignettes/data/A549_MYC_encTfChipPkENCFF542GMN_hg38.bed
vignettes/data/GM12878_chromHMM.bed.gz
vignettes/data/GREATv4.genes.hg19.tsv.gz
vignettes/data/tb_encTfChipPkENCFF215YWS_GM12878_MYB_hg19.bed
vignettes/data/tb_encTfChipPkENCFF369JAI_H1_hESC_RXRA_hg19.bed
vignettes/data/tb_encTfChipPkENCFF533NIV_A549_ELF1_hg19.bed
vignettes/data/tb_encTfChipPkENCFF708LCH_A549_JUN_hg19.bed
vignettes/group_associations.Rmd
vignettes/local-GREAT.Rmd
vignettes/online-GREAT.Rmd
vignettes/other-geneset-databases.Rmd
vignettes/other-organisms.Rmd
vignettes/rGREAT.Rmd
vignettes/suppl_compare_GO.Rmd
vignettes/suppl_compare_genome_versions.Rmd
vignettes/suppl_compare_online_and_local.Rmd
vignettes/suppl_compare_tss.Rmd
vignettes/suppl_use_background.Rmd
