Files in BioinformaticsFMRP/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/clinical.R R/download.R R/internal.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_DMR.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/calculate.pvalues.Rd man/chol_maf.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/diffmean.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/getMC3MAF.Rd man/getManifest.Rd man/getResults.Rd man/getSampleFilesSummary.Rd man/getTSS.Rd man/get_IDs.Rd man/ggbiplot.Rd man/isServeOK.Rd man/matchedMetExp.Rd man/met.gbm.27k.Rd man/msi_results.Rd man/pancan2018.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/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
BioinformaticsFMRP/TCGAbiolinks documentation built on Nov. 15, 2019, 11:28 a.m.