1. MethReg::clinical
    TCGA-COAD clinical matrix for 38 samples retrieved from GDC using TCGAbiolinks
    csv| xlsx| json| ndjson| rda| rds
    data.frame|38 x 4
  2. MethReg::dna.met.chr21
    TCGA-COAD DNA methylation matrix (beta-values) for 38 samples (only chr21) retrieved from GDC using TCGAbiolinks
    csv| json| rda| rds
    matrix|3012 x 38
  3. MethReg::gene.exp.chr21.log2
    TCGA-COAD gene expression matrix (log2 (FPKM-UQ + 1)) for 38 samples (only chromosome 21) retrieved from GDC using TCGAbiolinks
    csv| json| rda| rds
    matrix|752 x 38
  4. TCGAbiolinks::DE_PCBC_stemSig
    A numeric vector with SC-derived definitive endoderm (DE) signature trained on PCBC's dataset
    json| rda| rds
    numeric
  5. 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
  6. TCGAbiolinks::ECTO_PCBC_stemSig
    A numeric vector with SC-derived ectoderm (ECTO) signature trained on PCBC's dataset
    json| rda| rds
    numeric
  7. TCGAbiolinks::MESO_PCBC_stemSig
    A numeric vector with SC-derived mesoderm (MESO) signature trained on PCBC's dataset
    json| rda| rds
    numeric
  8. TCGAbiolinks::SC_PCBC_stemSig
    A numeric vector with stem cell-like signature trained on PCBC's dataset
    json| rda| rds
    numeric
  9. TCGAbiolinks::TabSubtypesCol_merged
    TCGA samples with their Pam50 subtypes
    csv| xlsx| json| ndjson| rda| rds
    data.frame|4768 x 3
  10. TCGAbiolinks::Tumor.purity
    TCGA samples with their Tumor Purity measures
    csv| xlsx| json| ndjson| rda| rds
    data.frame|9364 x 7
  11. TCGAbiolinks::bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf
    TCGA CHOL MAF
    csv| xlsx| json| ndjson| rda| rds
    tbl_df|3555 x 34
  12. TCGAbiolinks::chol_maf
    TCGA CHOL MAF transformed to maftools object
    rda| rds
    MAF
  13. TCGAbiolinks::clinical.biotab
    A list of data frames with clinical data parsed from XML (code in vignettes)
    json| rda| rds
    list
  14. TCGAbiolinks::dataBRCA
    TCGA data matrix BRCA
    csv| xlsx| json| ndjson| rda| rds
    data.frame|20530 x 10
  15. TCGAbiolinks::dataDEGsFiltLevel
    TCGA data matrix BRCA DEGs
    csv| xlsx| json| ndjson| rda| rds
    data.frame|3649 x 6
  16. TCGAbiolinks::dataREAD
    TCGA data SummarizedExperiment READ
    rda| rds
    RangedSummarizedExperiment
  17. TCGAbiolinks::dataREAD_df
    TCGA data matrix READ
    csv| xlsx| json| ndjson| rda| rds
    data.frame|20531 x 2
  18. TCGAbiolinks::gbm.exp.harmonized
    A RangedSummarizedExperiment two samples with gene expression data from vignette aligned against hg38
    rda| rds
    RangedSummarizedExperiment
  19. TCGAbiolinks::gbm.exp.legacy
    A RangedSummarizedExperiment two samples with gene expression data from vignette aligned against hg19
    rda| rds
    RangedSummarizedExperiment
  20. TCGAbiolinks::geneInfo
    geneInfo for normalization of RNAseq data
    csv| json| rda| rds
    matrix|20531 x 3
  21. TCGAbiolinks::geneInfoHT
    geneInfoHT for normalization of HTseq data
    csv| xlsx| json| ndjson| rda| rds
    data.frame|68016 x 2
  22. TCGAbiolinks::met.gbm.27k
    A DNA methylation RangedSummarizedExperiment for 8 samples (only first 20 probes) aligned against hg19
    rda| rds
    RangedSummarizedExperiment
  23. TCGAbiolinks::msi_results
    MSI data for two samples
    csv| xlsx| json| ndjson| rda| rds
    data.frame|2 x 4
  24. TCGAbiolinks::tabSurvKMcompleteDEGs
    tabSurvKMcompleteDEGs
    csv| xlsx| json| ndjson| rda| rds
    data.frame|200 x 7