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  1. TCGAbiolinks::bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf
    TCGA CHOL MAF
    csv| xlsx| json| ndjson| rda| rds
    tbl_df|3555 x 34
  2. TCGAbiolinks::chol_maf
    TCGA CHOL MAF transformed to maftools object
    rda| rds
    MAF
  3. TCGAbiolinks::clinical.biotab
    A list of data frames with clinical data parsed from XML (code in vignettes)
    json| rda| rds
    list
  4. TCGAbiolinks::dataBRCA
    TCGA data matrix BRCA
    csv| xlsx| json| ndjson| rda| rds
    data.frame|20530 x 10
  5. TCGAbiolinks::dataDEGsFiltLevel
    TCGA data matrix BRCA DEGs
    csv| xlsx| json| ndjson| rda| rds
    data.frame|3649 x 6
  6. TCGAbiolinks::dataREAD
    TCGA data SummarizedExperiment READ
    rda| rds
    RangedSummarizedExperiment
  7. TCGAbiolinks::dataREAD_df
    TCGA data matrix READ
    csv| xlsx| json| ndjson| rda| rds
    data.frame|20531 x 2
  8. TCGAbiolinks::DE_PCBC_stemSig
    A numeric vector with SC-derived definitive endoderm (DE) signature trained on PCBC's dataset
    json| rda| rds
    numeric
  9. TCGAbiolinks::EB_PCBC_stemSig
    A numeric vector with stem cell (SC)-derived embryoid bodies (EB) signature trained on PCBC's dataset
    json| rda| rds
    numeric
  10. TCGAbiolinks::ECTO_PCBC_stemSig
    A numeric vector with SC-derived ectoderm (ECTO) signature trained on PCBC's dataset
    json| rda| rds
    numeric
  11. TCGAbiolinks::gbm.exp.harmonized
    A RangedSummarizedExperiment two samples with gene expression data from vignette aligned against hg38
    rda| rds
    RangedSummarizedExperiment
  12. TCGAbiolinks::gbm.exp.legacy
    A RangedSummarizedExperiment two samples with gene expression data from vignette aligned against hg19
    rda| rds
    RangedSummarizedExperiment
  13. TCGAbiolinks::geneInfo
    geneInfo for normalization of RNAseq data
    csv| json| rda| rds
    matrix|20531 x 3
  14. TCGAbiolinks::geneInfoHT
    geneInfoHT for normalization of HTseq data
    csv| xlsx| json| ndjson| rda| rds
    data.frame|68016 x 2
  15. TCGAbiolinks::MESO_PCBC_stemSig
    A numeric vector with SC-derived mesoderm (MESO) signature trained on PCBC's dataset
    json| rda| rds
    numeric
  16. TCGAbiolinks::met.gbm.27k
    A DNA methylation RangedSummarizedExperiment for 8 samples (only first 20 probes) aligned against hg19
    rda| rds
    RangedSummarizedExperiment
  17. TCGAbiolinks::msi_results
    MSI data for two samples
    csv| xlsx| json| ndjson| rda| rds
    data.frame|2 x 4
  18. TCGAbiolinks::SC_PCBC_stemSig
    A numeric vector with stem cell-like signature trained on PCBC's dataset
    json| rda| rds
    numeric
  19. TCGAbiolinks::TabSubtypesCol_merged
    TCGA samples with their Pam50 subtypes
    csv| xlsx| json| ndjson| rda| rds
    data.frame|4768 x 3
  20. TCGAbiolinks::tabSurvKMcompleteDEGs
    tabSurvKMcompleteDEGs
    csv| xlsx| json| ndjson| rda| rds
    data.frame|200 x 7
  21. TCGAbiolinks::Tumor.purity
    TCGA samples with their Tumor Purity measures
    csv| xlsx| json| ndjson| rda| rds
    data.frame|9364 x 7
  22. TCGAWorkflowData::exp
    A gene expression matrix for 10 GBM and 10 LGG samples prepared for the creation of an ELMER object.
    rda| rds
    RangedSummarizedExperiment
  23. TCGAWorkflowData::exp_gbm
    A gene expression matrix with 20 GBM samples
    rda| rds
    RangedSummarizedExperiment
  24. TCGAWorkflowData::exp_lgg
    A gene expression matrix with 20 LGG samples
    rda| rds
    RangedSummarizedExperiment
  25. TCGAWorkflowData::gbm.samples
    Identifiers for the 10 GBM samples in the ELMER objects
    json| rda| rds
    character
  26. TCGAWorkflowData::genes
    A data frame object with gene information (hg19)
    csv| xlsx| json| ndjson| rda| rds
    data.frame|60482 x 4
  27. TCGAWorkflowData::genes_GR
    A GRanges object with gene information (hg19)
    rda| rds
    GRanges
  28. TCGAWorkflowData::gistic_allbygene
    A subset of GBM GISTIC2 results, which is used to identify genes targeted by somatic copy-number alterations (SCNAs) From: GDAC firehose, downloaded with RTCGAtoolbox
    csv| xlsx| json| ndjson| rda| rds
    data.frame|24776 x 0
  29. TCGAWorkflowData::gistic_thresholedbygene
    A subset of GBM GISTIC2 results, which is used to identify genes targeted by somatic copy-number alterations (SCNAs) From: GDAC firehose, downloaded with RTCGAtoolbox
    csv| xlsx| json| ndjson| rda| rds
    data.frame|24776 x 0
  30. TCGAWorkflowData::histone.marks
    histone marks specific for brain tissue from the Roadmap database.
    rda| rds
    list
  31. TCGAWorkflowData::lgg.samples
    Identifiers for the 10 LGG samples in the ELMER objects
    json| rda| rds
    character
  32. TCGAWorkflowData::maf
    Merged LGG and GBM GDC MAF files from GDC workflow: Aliquot Ensemble Somatic Variant Merging and Masking
    csv| xlsx| json| ndjson| rda| rds
    data.frame|87957 x 141
  33. TCGAWorkflowData::met
    A SummarizedExperiment containing TCGA data: DNA methylation platform 450K chromossome 9 for 10 LGG samples and 10 GBM samples
    rda| rds
    RangedSummarizedExperiment
  34. TCGAWorkflowData::met
    A SummarizedExperiment containing TCGA data: DNA methylation platform 450K chromossome 9 for 10 LGG samples and 10 GBM samples
    rda| rds
    RangedSummarizedExperiment
  35. TCGAWorkflowData::tmp.biogrid
    Biogrid information
    csv| xlsx| json| ndjson| rda| rds
    data.frame|1379810 x 24