1. COCOA::atf3_chr1
    Atf3 binding regions.
    rda| rds
    GRanges
  2. COCOA::brcaATACCoord1
    A GRanges object with coordinates for select BRCA ATAC-seq peak regions from chr1.
    rda| rds
    GRanges
  3. COCOA::brcaATACData1
    A matrix with ATAC-seq counts in select peak regions from chromosome 1 for 37 patients.
    csv| json| rda| rds
    matrix|4053 x 37
  4. COCOA::brcaMCoord1
    A GRanges object with genomic coordinates for cytosines from chr1 for the package's built-in DNA methylation data
    rda| rds
    GRanges
  5. COCOA::brcaMetadata
    A data.frame with patient metadata for breast cancer patients.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|329 x 6
  6. COCOA::brcaMethylData1
    A matrix with DNA methylation levels from some CpGs on chromosome 1
    csv| json| rda| rds
    matrix|6004 x 300
  7. COCOA::brcaPCScores
    A matrix with principal component scores for PCs 1-4 for four breast cancer patients.
    csv| json| rda| rds
    matrix|4 x 4
  8. COCOA::brcaPCScores657
    A data.frame with principal component scores for PCs 1-4 for 657 breast cancer patients as well as a column with estrogen receptor status.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|657 x 5
  9. COCOA::esr1_chr1
    Estrogen receptor alpha binding regions.
    rda| rds
    GRanges
  10. COCOA::gata3_chr1
    Gata3 binding regions.
    rda| rds
    GRanges
  11. COCOA::nrf1_chr1
    Nrf1 binding regions.
    rda| rds
    GRanges
  12. COCOA::rsScores
    Example COCOA Results (made up)
    csv| xlsx| json| ndjson| rda| rds
    data.frame|5 x 3
  13. GenomicDistributions::TSS_hg19
    hg19 TSS locations
    rda| rds
    GRanges
  14. GenomicDistributions::cellTypeMetadata
    Table the maps cell types to tissues and groups
    csv| xlsx| json| ndjson| rda| rds
    data.table|112 x 3
  15. GenomicDistributions::chromSizes_hg19
    hg19 chromosome sizes
    json| rda| rds
    integer
  16. GenomicDistributions::exampleOpenSignalMatrix_hg19
    A dataset containing a subset of open chromatin regions across all cell types defined by ENCODE for Homo Sapiens hg19
    csv| xlsx| json| ndjson| rda| rds
    data.table|100 x 14
  17. GenomicDistributions::geneModels_hg19
    hg38 gene models
    rda| rds
    list
  18. GenomicDistributions::setB_100
    Example BED file read with rtracklayer::import
    rda| rds
    GRanges
  19. GenomicDistributions::vistaEnhancers
    Example BED file read with rtracklayer::import
    rda| rds
    GRanges
  20. MIRA::bigBinDT1
    DNA methylation data for the "Applying MIRA to a Biological Question" vignette (1st part).
    csv| xlsx| json| ndjson| rda| rds
    data.table|252 x 5
  21. MIRA::bigBinDT2
    DNA methylation data for the "Applying MIRA to a Biological Question" vignette (2nd part).
    csv| xlsx| json| ndjson| rda| rds
    data.table|1008 x 5
  22. MIRA::exampleAnnoDT1
    A data.table with annotation for a bisulfite sample.
    csv| xlsx| json| ndjson| rda| rds
    data.table|1 x 2
  23. MIRA::exampleAnnoDT2
    Annotation data for the "Applying MIRA to a Biological Question" vignette.
    csv| xlsx| json| ndjson| rda| rds
    data.table|24 x 2
  24. MIRA::exampleBSDT
    A data.table containing DNA methylation data.
    csv| xlsx| json| ndjson| rda| rds
    data.table|4000 x 4
  25. MIRA::exampleBSseqObj
    A small BSseq object.
    rda| rds
    BSseq
  26. MIRA::exampleBins
    A data.table with artificial binned methylation data
    csv| xlsx| json| ndjson| rda| rds
    data.table|22 x 6
  27. MIRA::exampleRegionSet
    A Granges object with Nrf1-binding regions.
    rda| rds
    GRanges