├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── DPA.R ├── FEA.R ├── GRN.R ├── GSEA.R ├── LPA.R ├── MoonlightR.R ├── PRA.R ├── URA.R ├── getDataGEO.R ├── getDataTCGA.R ├── moonlight.R ├── plotCircos.R ├── plotFEA.R ├── plotNetworkHive.R └── plotURA.R ├── README.md ├── appveyor.yml ├── data ├── DEGsmatrix.rda ├── DiseaseList.rda ├── EAGenes.rda ├── GDCprojects.rda ├── GEO_TCGAtab.rda ├── dataFilt.rda ├── dataGRN.rda ├── dataURA.rda ├── datalist ├── geneInfo.rda ├── knownDriverGenes.rda ├── listMoonlight.rda └── tabGrowBlock.rda ├── inst └── CITATION ├── man ├── DEGsmatrix.Rd ├── DPA.Rd ├── DiseaseList.Rd ├── EAGenes.Rd ├── FEA.Rd ├── GDCprojects.Rd ├── GEO_TCGAtab.Rd ├── GRN.Rd ├── GSEA.Rd ├── LPA.Rd ├── MoonlightR.Rd ├── PRA.Rd ├── URA.Rd ├── dataFilt.Rd ├── dataGRN.Rd ├── dataURA.Rd ├── geneInfo.Rd ├── getDataGEO.Rd ├── getDataTCGA.Rd ├── knownDriverGenes.Rd ├── listMoonlight.Rd ├── moonlight.Rd ├── plotCircos.Rd ├── plotFEA.Rd ├── plotNetworkHive.Rd ├── plotURA.Rd └── tabGrowBlock.Rd └── vignettes ├── Case1_URA.png ├── DEGs_volcano.png ├── FEAplot.png ├── GSEAplot.png ├── Moonlight.Rmd ├── Moonlight_Pipeline.png ├── URAplot.png ├── circos_ocg_tsg_ncancer5.png ├── circos_ocg_tsg_stages.png └── networkHive.png /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/MoonlightR/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/MoonlightR/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/MoonlightR/HEAD/.travis.yml 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