Files in daniel615212950/TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
.Rapp.history
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/Pam50Info.R
R/TCGAbiolinks.R
R/TumorPurityInfo.R
R/analyze.R
R/api.R
R/biomart.R
R/classifiers.R
R/clinical.R
R/download.R
R/internal.R
R/linkedOmics.R
R/methylation.R
R/prepare.R
R/query.R
R/sysdata.rda
R/visualize.R
README.md
TCGAbiolinks.Rproj
appveyor.yml
data/PCBC_stemSig.rda
data/TabSubtypesCol_merged.rda
data/Tumor.purity.rda
data/bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf.rda
data/chol_maf.rda
data/clinical.biotab.rda
data/dataBRCA.rda
data/dataDEGsFiltLevel.rda
data/dataREAD.rda
data/dataREAD_df.rda
data/datalist
data/gbm.exp.harmonized.rda
data/gbm.exp.legacy.rda
data/geneInfo.rda
data/geneInfoHT.rda
data/met.gbm.27k.rda
data/msi_results.rda
data/tabSurvKMcompleteDEGs.rda
inst/CITATION
man/.Rapp.history
man/BRCA_rnaseqv2.Rd
man/GDCdownload.Rd
man/GDCprepare.Rd
man/GDCprepare_clinic.Rd
man/GDCquery.Rd
man/GDCquery_ATAC_seq.Rd
man/GDCquery_Maf.Rd
man/GDCquery_clinic.Rd
man/GeneSplitRegulon.Rd
man/GenesCutID.Rd
man/PCBC_stemSig.Rd
man/PanCancerAtlas_subtypes.Rd
man/TCGAVisualize_volcano.Rd
man/TCGA_MolecularSubtype.Rd
man/TCGAanalyze_Clustering.Rd
man/TCGAanalyze_DEA.Rd
man/TCGAanalyze_DEA_Affy.Rd
man/TCGAanalyze_DMC.Rd
man/TCGAanalyze_EA.Rd
man/TCGAanalyze_EAcomplete.Rd
man/TCGAanalyze_Filtering.Rd
man/TCGAanalyze_LevelTab.Rd
man/TCGAanalyze_Normalization.Rd
man/TCGAanalyze_Pathview.Rd
man/TCGAanalyze_Preprocessing.Rd
man/TCGAanalyze_Stemness.Rd
man/TCGAanalyze_SurvivalKM.Rd
man/TCGAanalyze_analyseGRN.Rd
man/TCGAanalyze_networkInference.Rd
man/TCGAanalyze_survival.Rd
man/TCGAbatch_Correction.Rd
man/TCGAbiolinks.Rd
man/TCGAprepare_Affy.Rd
man/TCGAquery_MatchedCoupledSampleTypes.Rd
man/TCGAquery_SampleTypes.Rd
man/TCGAquery_recount2.Rd
man/TCGAquery_subtype.Rd
man/TCGAtumor_purity.Rd
man/TCGAvisualize_BarPlot.Rd
man/TCGAvisualize_EAbarplot.Rd
man/TCGAvisualize_Heatmap.Rd
man/TCGAvisualize_PCA.Rd
man/TCGAvisualize_SurvivalCoxNET.Rd
man/TCGAvisualize_meanMethylation.Rd
man/TCGAvisualize_oncoprint.Rd
man/TCGAvisualize_starburst.Rd
man/TabSubtypesCol_merged.Rd
man/Tumor.purity.Rd
man/UseRaw_afterFilter.Rd
man/batch.info.Rd
man/bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf.Rd
man/chol_maf.Rd
man/classification.Rd
man/clinBRCA.Rd
man/clinical.biotab.Rd
man/colDataPrepare.Rd
man/dataBRCA.Rd
man/dataDEGsFiltLevel.Rd
man/dataREAD.Rd
man/dataREAD_df.Rd
man/dmc.non.parametric.Rd
man/dmc.non.parametric.se.Rd
man/gaiaCNVplot.Rd
man/gbm.exp.harmonized.Rd
man/gbm.exp.legacy.Rd
man/geneInfo.Rd
man/geneInfoHT.Rd
man/get.GRCh.bioMart.Rd
man/getAdjacencyBiogrid.Rd
man/getDataCategorySummary.Rd
man/getGDCInfo.Rd
man/getGDCprojects.Rd
man/getGistic.Rd
man/getLinkedOmicsData.Rd
man/getMC3MAF.Rd
man/getManifest.Rd
man/getNbCases.Rd
man/getNbFiles.Rd
man/getProjectSummary.Rd
man/getResults.Rd
man/getSampleFilesSummary.Rd
man/getTSS.Rd
man/get_IDs.Rd
man/ggbiplot.Rd
man/gliomaClassifier.Rd
man/isServeOK.Rd
man/matchedMetExp.Rd
man/met.gbm.27k.Rd
man/msi_results.Rd
man/pancan2018.Rd
man/splitAPICall.Rd
man/tabSurvKMcompleteDEGs.Rd
tests/testthat.R
tests/testthat/test-analyse.R
tests/testthat/test-prepare-download.R
tests/testthat/test-query-clinical.R
tests/testthat/test-query.R
tests/testthat/test-visualize.R
vignettes/.install_extras
vignettes/BRCA_cluster.png
vignettes/BRCA_heatmap.png
vignettes/CIMP-highvsCIMP-low_metvolcano.png
vignettes/EAplot.png
vignettes/PCAtop200DEGs.png
vignettes/PreprocessingOutput.png
vignettes/_output.yaml
vignettes/_site.yml
vignettes/analysis.Rmd
vignettes/bibliography.bib
vignettes/case1_EA.png
vignettes/case1_dnet.png
vignettes/case2_Heatmap.jpg
vignettes/case2_surv.png
vignettes/case4_elmer.png
vignettes/casestudy.Rmd
vignettes/classifiers.Rmd
vignettes/clinical.Rmd
vignettes/download_prepare.Rmd
vignettes/elmer1.png
vignettes/elmer2.jpg
vignettes/elmer3.png
vignettes/elmer4.png
vignettes/extension.Rmd
vignettes/figure4cluster.png
vignettes/figure4surv.png
vignettes/figure5exp.png
vignettes/figure5met.png
vignettes/figure5star.png
vignettes/gui.Rmd
vignettes/include/after_body.html
vignettes/include/before_body.html
vignettes/include/header.html
vignettes/include/logo.png
vignettes/include/site.css
vignettes/include/symbol.png
vignettes/index.Rmd
vignettes/mutation.Rmd
vignettes/oncoprint.png
vignettes/query.Rmd
vignettes/subtypes.Rmd
