API for TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
| Global functions | |
|---|---|
| .fun | Source code |
| .quantileNormalization | Source code |
| BRCA_rnaseqv2 | Man page |
| GDCclientExists | Source code |
| GDCclientInstall | Source code |
| GDCclientPath | Source code |
| GDCdownload | Man page Source code |
| GDCdownload.aux | Source code |
| GDCdownload.by.chunk | Source code |
| GDCprepare | Man page Source code |
| GDCprepare_clinic | Man page Source code |
| GDCquery | Man page Source code |
| GDCquery_ATAC_seq | Man page Source code |
| GDCquery_Maf | Man page Source code |
| GDCquery_clinic | Man page Source code |
| GeneSplitRegulon | Man page Source code |
| GenesCutID | Man page Source code |
| PCBC_stemSig | Man page |
| PanCancerAtlas_subtypes | Man page |
| TCGAVisualize_volcano | Man page |
| TCGA_MolecularSubtype | Man page |
| TCGAanalyze_Clustering | Man page Source code |
| TCGAanalyze_DEA | Man page |
| TCGAanalyze_DEA_Affy | Man page Source code |
| TCGAanalyze_DMC | Man page |
| TCGAanalyze_EA | Man page |
| TCGAanalyze_EAcomplete | Man page Source code |
| TCGAanalyze_Filtering | Man page Source code |
| TCGAanalyze_LevelTab | Man page Source code |
| TCGAanalyze_Normalization | Man page Source code |
| TCGAanalyze_Pathview | Man page Source code |
| TCGAanalyze_Preprocessing | Man page Source code |
| TCGAanalyze_Stemness | Man page Source code |
| TCGAanalyze_SurvivalKM | Man page Source code |
| TCGAanalyze_analyseGRN | Man page Source code |
| TCGAanalyze_networkInference | Man page Source code |
| TCGAanalyze_survival | Man page Source code |
| TCGAbatch_Correction | Man page |
| TCGAbiolinks | Man page |
| TCGAprepare_Affy | Man page Source code |
| TCGAquery_MatchedCoupledSampleTypes | Man page Source code |
| TCGAquery_SampleTypes | Man page Source code |
| TCGAquery_recount2 | Man page Source code |
| TCGAquery_subtype | Man page |
| TCGAtumor_purity | Man page |
| TCGAvisualize_BarPlot | Man page Source code |
| TCGAvisualize_EAbarplot | Man page Source code |
| TCGAvisualize_Heatmap | Man page Source code |
| TCGAvisualize_PCA | Man page Source code |
| TCGAvisualize_SurvivalCoxNET | Man page Source code |
| TCGAvisualize_meanMethylation | Man page Source code |
| TCGAvisualize_oncoprint | Man page Source code |
| TCGAvisualize_starburst | Man page |
| TabSubtypesCol_merged | Man page |
| Tumor.purity | Man page |
| UseRaw_afterFilter | Man page Source code |
| addFFPE | Source code |
| addFilter | Source code |
| addSubtypeInfo | Source code |
| batch.info | Man page |
| bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf | Man page |
| checkAlreadyDownloaded | Source code |
| checkBarcodeDefinition | Source code |
| checkDataCategoriesInput | Source code |
| checkDataTypeInput | Source code |
| checkLegacyPlatform | Source code |
| checkProjectInput | Source code |
| check_package | Source code |
| chol_maf | Man page |
| classification | Man page |
| clinBRCA | Man page |
| clinical.biotab | Man page |
| colDataPrepare | Man page Source code |
| colDataPrepareMMRF | Source code |
| colDataPrepareTARGET | Source code |
| colDataPrepareTCGA | Source code |
| dataBRCA | Man page |
| dataDEGsFiltLevel | Man page |
| dataREAD | Man page |
| dataREAD_df | Man page |
| dmc.non.parametric | Man page |
| dmc.non.parametric.se | Man page |
| expandBarcodeInfo | Source code |
| gaiaCNVplot | Man page |
| gbm.exp.harmonized | Man page |
| gbm.exp.legacy | Man page |
| geneInfo | Man page |
| geneInfoHT | Man page |
| get.GRCh.bioMart | Man page Source code |
| get.cnv | Source code |
| get.mut.gistc | Source code |
| get.mut.gistc.information | Source code |
| get.mutation | Source code |
| getAdjacencyBiogrid | Man page Source code |
| getAliquot_ids | Source code |
| getBarcodeDefinition | Source code |
| getBarcodeInfo | Source code |
| getBarcodefromAliquot | Source code |
| getDataCategorySummary | Man page Source code |
| getFFPE | Source code |
| getGDCInfo | Man page Source code |
| getGDCprojects | Man page Source code |
| getGDCquery | Source code |
| getGistic | Man page Source code |
| getInfiniumAnnotation | Source code |
| getLinkedOmicsData | Man page Source code |
| getMC3MAF | Man page Source code |
| getManifest | Man page Source code |
| getNbCases | Man page Source code |
| getNbFiles | Man page Source code |
| getProjectSummary | Man page Source code |
| getResults | Man page Source code |
| getSampleFilesSummary | Man page Source code |
| getSampleSummaryUrl | Source code |
| getSubmitterID | Source code |
| getSubmitterIDUrl | Source code |
| getTSS | Man page Source code |
| getURL | Source code |
| get_IDs | Man page Source code |
| ggbiplot | Man page Source code |
| gliomaClassifier | Man page Source code |
| humanReadableByteCount | Source code |
| is.linux | Source code |
| is.mac | Source code |
| is.windows | Source code |
| isServeOK | Man page Source code |
| makeSEFromDNAMethylationMatrix | Source code |
| makeSEfromDNAmethylation | Source code |
| makeSEfromGeneExpressionQuantification | Source code |
| makeSEfromTranscriptomeProfiling | Source code |
| makeSEfromTranscriptomeProfilingSTAR | Source code |
| map.ensg | Source code |
| matchedMetExp | Man page Source code |
| met.gbm.27k | Man page |
| move | Source code |
| msi_results | Man page |
| pancan2018 | Man page |
| print.header | Source code |
| readClinical | Source code |
| readCopyNumberVariation | Source code |
| readDNAmethylation | Source code |
| readGISTIC | Source code |
| readGeneExpressionQuantification | Source code |
| readIDATDNAmethylation | Source code |
| readProteinExpression | Source code |
| readSimpleNucleotideVariationMaf | Source code |
| readTranscriptomeProfiling | Source code |
| remove.files.recursively | Source code |
| set_cores | Source code |
| splitAPICall | Man page Source code |
| tabSurvKMcompleteDEGs | Man page |
| unlistlabels | Source code |
