├── .DS_Store ├── .RData ├── .Rapp.history ├── .gitignore ├── README.md ├── Scripts ├── .DS_Store ├── Downloading_DataPreparation.Rmd ├── Libraries_HelperFunctions_ForBRCAVignette.R ├── Libraries_HelperFunctions_ForTcgaReadVignette.R ├── RLibraries_HelperFunctions_ForMultipleStudies.R ├── RLibraries_HelperFunctions_ForPaper.Rmd ├── RUV_III_PRPS_Multiples_Studies.Rmd ├── Statistical_Summaries_AllTCGACancerTypes.Rmd ├── TCGA_BRCA_RNAseq.Rmd ├── TCGA_BRCA_RNAseq_Vignette.Rmd ├── TCGA_COAD_RNAseq.Rmd ├── TCGA_LibrarySizeNormalization-SingleBatch_Vignette.Rmd ├── TCGA_LibrarySizeNormalization_SingleBatach.Rmd ├── TCGA_READ_RNAseq.Rmd ├── TCGA_READ_RNAseq_Vignette.Rmd ├── TCGA_READ_RNAseq_tcgaCleaneR_Vignette.Rmd ├── TCGA_REDA_OtherNormalization.Rmd └── UnwantedVariation_AllTCGACancerTypes.Rmd ├── TCGA_Main1.png ├── TCGA_PanCancer_UnwantedVariation.Rproj ├── TCGA_RShiny ├── Libraries_HelperFunctions_ForRshiny.R └── Rshiny_TCGA_PanCancer_RNAseq_UwantedVariation.R ├── Vigettes ├── .DS_Store ├── TCGA_BRCA_RNAseq_Vignette.html └── TCGA_READ_RNAseq_Vignette.html └── tcgaCleaneR ├── .DS_Store ├── DESCRIPTION ├── NAMESPACE ├── R ├── Anova.R ├── PCA.R ├── Plot_PCA.R ├── RUV_III.R ├── brca.data.R ├── checkNCG.R ├── filter_genes.R ├── filter_low_genes.R ├── gene_correlation.R ├── library.size.R ├── library_size_filter.R ├── pc_reg_corr.R ├── purity_filter.R ├── ruv_prps.R ├── ruv_prps_plot.R └── study_design.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── data └── brca.data.rda ├── data_raw └── tgca_breast_cancer_data.R ├── docs ├── 404.html ├── articles │ ├── index.html │ ├── tcgaCleaneR_vignette.html │ └── tcgaCleaneR_vignette_files │ │ ├── figure-html │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-14-1.png │ │ ├── unnamed-chunk-14-2.png │ │ ├── unnamed-chunk-14-3.png │ │ ├── unnamed-chunk-15-1.png │ │ ├── unnamed-chunk-16-1.png │ │ ├── unnamed-chunk-18-1.png │ │ ├── unnamed-chunk-19-1.png │ │ ├── unnamed-chunk-26-1.png │ │ └── unnamed-chunk-8-1.png │ │ └── header-attrs-2.11 │ │ └── header-attrs.js ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── brca.data.html │ ├── checkNegCtrlGenes.html │ ├── computeANOVA.html │ ├── computeCorr.html │ ├── computePCA.html │ ├── createPRPS.html │ ├── figures │ │ ├── README-unnamed-chunk-10-1.png │ │ ├── README-unnamed-chunk-14-1.png │ │ ├── README-unnamed-chunk-14-2.png │ │ ├── README-unnamed-chunk-14-3.png │ │ ├── README-unnamed-chunk-15-1.png │ │ ├── README-unnamed-chunk-16-1.png │ │ ├── README-unnamed-chunk-23-1.png │ │ └── README-unnamed-chunk-8-1.png │ ├── filterGenesByBiotypes.html │ ├── filterLowExprGenes.html │ ├── filterSamplesByLibSize.html │ ├── filterSamplesByPurity.html │ ├── index.html │ ├── plotLibSize-1.png │ ├── plotLibSize.html │ ├── plotPC.html │ ├── plotPCsVar.html │ ├── plotPRPS.html │ ├── plotStudyOutline.html │ ├── runRUVIII.html │ └── runRUV_III_PRPS.html └── sitemap.xml ├── man ├── brca.data.Rd ├── checkNegCtrlGenes.Rd ├── computeANOVA.Rd ├── computeCorr.Rd ├── computePCA.Rd ├── createPRPS.Rd ├── figures │ ├── README-unnamed-chunk-10-1.png │ ├── README-unnamed-chunk-14-1.png │ ├── README-unnamed-chunk-14-2.png │ ├── README-unnamed-chunk-14-3.png │ ├── README-unnamed-chunk-15-1.png │ ├── README-unnamed-chunk-16-1.png │ ├── README-unnamed-chunk-23-1.png │ └── README-unnamed-chunk-8-1.png ├── filterGenesByBiotypes.Rd ├── filterLowExprGenes.Rd ├── filterSamplesByLibSize.Rd ├── filterSamplesByPurity.Rd ├── plotLibSize.Rd ├── plotPC.Rd ├── plotPCsVar.Rd ├── plotPRPS.Rd ├── plotStudyOutline.Rd ├── runRUVIII.Rd └── runRUV_III_PRPS.Rd └── vignettes ├── .gitignore └── tcgaCleaneR_vignette.Rmd /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/.DS_Store -------------------------------------------------------------------------------- /.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/.RData -------------------------------------------------------------------------------- /.Rapp.history: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/.Rapp.history -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/README.md -------------------------------------------------------------------------------- /Scripts/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/.DS_Store -------------------------------------------------------------------------------- /Scripts/Downloading_DataPreparation.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/Downloading_DataPreparation.Rmd -------------------------------------------------------------------------------- /Scripts/Libraries_HelperFunctions_ForBRCAVignette.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/Libraries_HelperFunctions_ForBRCAVignette.R -------------------------------------------------------------------------------- /Scripts/Libraries_HelperFunctions_ForTcgaReadVignette.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/Libraries_HelperFunctions_ForTcgaReadVignette.R -------------------------------------------------------------------------------- /Scripts/RLibraries_HelperFunctions_ForMultipleStudies.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/RLibraries_HelperFunctions_ForMultipleStudies.R -------------------------------------------------------------------------------- /Scripts/RLibraries_HelperFunctions_ForPaper.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/RLibraries_HelperFunctions_ForPaper.Rmd -------------------------------------------------------------------------------- /Scripts/RUV_III_PRPS_Multiples_Studies.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/RUV_III_PRPS_Multiples_Studies.Rmd -------------------------------------------------------------------------------- /Scripts/Statistical_Summaries_AllTCGACancerTypes.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/Statistical_Summaries_AllTCGACancerTypes.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_BRCA_RNAseq.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_BRCA_RNAseq.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_BRCA_RNAseq_Vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_BRCA_RNAseq_Vignette.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_COAD_RNAseq.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_COAD_RNAseq.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_LibrarySizeNormalization-SingleBatch_Vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_LibrarySizeNormalization-SingleBatch_Vignette.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_LibrarySizeNormalization_SingleBatach.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_LibrarySizeNormalization_SingleBatach.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_READ_RNAseq.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_READ_RNAseq.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_READ_RNAseq_Vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_READ_RNAseq_Vignette.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_READ_RNAseq_tcgaCleaneR_Vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_READ_RNAseq_tcgaCleaneR_Vignette.Rmd -------------------------------------------------------------------------------- /Scripts/TCGA_REDA_OtherNormalization.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/TCGA_REDA_OtherNormalization.Rmd -------------------------------------------------------------------------------- /Scripts/UnwantedVariation_AllTCGACancerTypes.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Scripts/UnwantedVariation_AllTCGACancerTypes.Rmd -------------------------------------------------------------------------------- /TCGA_Main1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/TCGA_Main1.png -------------------------------------------------------------------------------- /TCGA_PanCancer_UnwantedVariation.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/TCGA_PanCancer_UnwantedVariation.Rproj -------------------------------------------------------------------------------- /TCGA_RShiny/Libraries_HelperFunctions_ForRshiny.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/TCGA_RShiny/Libraries_HelperFunctions_ForRshiny.R -------------------------------------------------------------------------------- /TCGA_RShiny/Rshiny_TCGA_PanCancer_RNAseq_UwantedVariation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/TCGA_RShiny/Rshiny_TCGA_PanCancer_RNAseq_UwantedVariation.R -------------------------------------------------------------------------------- /Vigettes/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Vigettes/.DS_Store -------------------------------------------------------------------------------- /Vigettes/TCGA_BRCA_RNAseq_Vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Vigettes/TCGA_BRCA_RNAseq_Vignette.html -------------------------------------------------------------------------------- /Vigettes/TCGA_READ_RNAseq_Vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/Vigettes/TCGA_READ_RNAseq_Vignette.html -------------------------------------------------------------------------------- /tcgaCleaneR/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/.DS_Store -------------------------------------------------------------------------------- /tcgaCleaneR/DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/DESCRIPTION -------------------------------------------------------------------------------- /tcgaCleaneR/NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/NAMESPACE -------------------------------------------------------------------------------- /tcgaCleaneR/R/Anova.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/Anova.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/PCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/PCA.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/Plot_PCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/Plot_PCA.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/RUV_III.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/RUV_III.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/brca.data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/brca.data.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/checkNCG.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/checkNCG.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/filter_genes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/filter_genes.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/filter_low_genes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/filter_low_genes.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/gene_correlation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/gene_correlation.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/library.size.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/library.size.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/library_size_filter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/library_size_filter.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/pc_reg_corr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/pc_reg_corr.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/purity_filter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/purity_filter.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/ruv_prps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/ruv_prps.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/ruv_prps_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/ruv_prps_plot.R -------------------------------------------------------------------------------- /tcgaCleaneR/R/study_design.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/R/study_design.R -------------------------------------------------------------------------------- /tcgaCleaneR/README.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/README.Rmd -------------------------------------------------------------------------------- /tcgaCleaneR/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/README.md -------------------------------------------------------------------------------- /tcgaCleaneR/_pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/_pkgdown.yml -------------------------------------------------------------------------------- /tcgaCleaneR/data/brca.data.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/data/brca.data.rda -------------------------------------------------------------------------------- /tcgaCleaneR/data_raw/tgca_breast_cancer_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/data_raw/tgca_breast_cancer_data.R -------------------------------------------------------------------------------- /tcgaCleaneR/docs/404.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/404.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/index.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-10-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-10-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-14-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-14-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-14-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-14-2.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-14-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-14-3.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-15-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-15-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-16-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-16-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-18-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-18-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-19-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-19-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-26-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-26-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/figure-html/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/header-attrs-2.11/header-attrs.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/articles/tcgaCleaneR_vignette_files/header-attrs-2.11/header-attrs.js -------------------------------------------------------------------------------- /tcgaCleaneR/docs/authors.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/authors.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/bootstrap-toc.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/bootstrap-toc.css -------------------------------------------------------------------------------- /tcgaCleaneR/docs/bootstrap-toc.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/bootstrap-toc.js -------------------------------------------------------------------------------- /tcgaCleaneR/docs/docsearch.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/docsearch.css -------------------------------------------------------------------------------- /tcgaCleaneR/docs/docsearch.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/docsearch.js -------------------------------------------------------------------------------- /tcgaCleaneR/docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/index.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/link.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/link.svg -------------------------------------------------------------------------------- /tcgaCleaneR/docs/pkgdown.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/pkgdown.css -------------------------------------------------------------------------------- /tcgaCleaneR/docs/pkgdown.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/pkgdown.js -------------------------------------------------------------------------------- /tcgaCleaneR/docs/pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/pkgdown.yml -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/Rplot001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/Rplot001.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/brca.data.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/brca.data.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/checkNegCtrlGenes.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/checkNegCtrlGenes.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/computeANOVA.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/computeANOVA.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/computeCorr.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/computeCorr.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/computePCA.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/computePCA.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/createPRPS.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/createPRPS.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-10-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-10-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-14-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-14-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-14-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-14-2.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-14-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-14-3.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-15-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-15-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-16-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-16-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-23-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-23-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/figures/README-unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/filterGenesByBiotypes.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/filterGenesByBiotypes.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/filterLowExprGenes.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/filterLowExprGenes.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/filterSamplesByLibSize.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/filterSamplesByLibSize.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/filterSamplesByPurity.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/filterSamplesByPurity.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/index.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/plotLibSize-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/plotLibSize-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/plotLibSize.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/plotLibSize.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/plotPC.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/plotPC.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/plotPCsVar.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/plotPCsVar.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/plotPRPS.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/plotPRPS.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/plotStudyOutline.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/plotStudyOutline.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/runRUVIII.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/runRUVIII.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/reference/runRUV_III_PRPS.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/reference/runRUV_III_PRPS.html -------------------------------------------------------------------------------- /tcgaCleaneR/docs/sitemap.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/docs/sitemap.xml -------------------------------------------------------------------------------- /tcgaCleaneR/man/brca.data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/brca.data.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/checkNegCtrlGenes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/checkNegCtrlGenes.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/computeANOVA.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/computeANOVA.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/computeCorr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/computeCorr.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/computePCA.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/computePCA.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/createPRPS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/createPRPS.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/figures/README-unnamed-chunk-10-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/figures/README-unnamed-chunk-10-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/man/figures/README-unnamed-chunk-14-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/figures/README-unnamed-chunk-14-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/man/figures/README-unnamed-chunk-14-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/figures/README-unnamed-chunk-14-2.png -------------------------------------------------------------------------------- /tcgaCleaneR/man/figures/README-unnamed-chunk-14-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/figures/README-unnamed-chunk-14-3.png -------------------------------------------------------------------------------- /tcgaCleaneR/man/figures/README-unnamed-chunk-15-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/figures/README-unnamed-chunk-15-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/man/figures/README-unnamed-chunk-16-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/figures/README-unnamed-chunk-16-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/man/figures/README-unnamed-chunk-23-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/figures/README-unnamed-chunk-23-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/man/figures/README-unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/figures/README-unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /tcgaCleaneR/man/filterGenesByBiotypes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/filterGenesByBiotypes.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/filterLowExprGenes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/filterLowExprGenes.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/filterSamplesByLibSize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/filterSamplesByLibSize.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/filterSamplesByPurity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/filterSamplesByPurity.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/plotLibSize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/plotLibSize.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/plotPC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/plotPC.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/plotPCsVar.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/plotPCsVar.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/plotPRPS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/plotPRPS.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/plotStudyOutline.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/plotStudyOutline.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/runRUVIII.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/runRUVIII.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/man/runRUV_III_PRPS.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/man/runRUV_III_PRPS.Rd -------------------------------------------------------------------------------- /tcgaCleaneR/vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | *.R 3 | -------------------------------------------------------------------------------- /tcgaCleaneR/vignettes/tcgaCleaneR_vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RMolania/TCGA_PanCancer_UnwantedVariation/HEAD/tcgaCleaneR/vignettes/tcgaCleaneR_vignette.Rmd --------------------------------------------------------------------------------