1. consensusSeekeR::A549_CTCF_MYJ_NarrowPeaks_partial
    Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
    rda| rds
    GRanges
  2. consensusSeekeR::A549_CTCF_MYJ_Peaks_partial
    Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
    rda| rds
    GRanges
  3. consensusSeekeR::A549_CTCF_MYN_NarrowPeaks_partial
    Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
    rda| rds
    GRanges
  4. consensusSeekeR::A549_CTCF_MYN_Peaks_partial
    Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
    rda| rds
    GRanges
  5. consensusSeekeR::A549_FOSL2_01_NarrowPeaks_partial
    Genomic regions with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)
    rda| rds
    GRanges
  6. consensusSeekeR::A549_FOSL2_01_Peaks_partial
    Sites with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)
    rda| rds
    GRanges
  7. consensusSeekeR::A549_FOXA1_01_NarrowPeaks_partial
    Genomic regions with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)
    rda| rds
    GRanges
  8. consensusSeekeR::A549_FOXA1_01_Peaks_partial
    Sites with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)
    rda| rds
    GRanges
  9. consensusSeekeR::A549_NR3C1_CFQ_NarrowPeaks_partial
    Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.
    rda| rds
    GRanges
  10. consensusSeekeR::A549_NR3C1_CFQ_Peaks_partial
    Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.
    rda| rds
    GRanges
  11. consensusSeekeR::A549_NR3C1_CFR_NarrowPeaks_partial
    Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.
    rda| rds
    GRanges
  12. consensusSeekeR::A549_NR3C1_CFR_Peaks_partial
    Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.
    rda| rds
    GRanges
  13. consensusSeekeR::A549_NR3C1_CFS_NarrowPeaks_partial
    Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFS). For demonstration purpose.
    rda| rds
    GRanges
  14. consensusSeekeR::A549_NR3C1_CFS_Peaks_partial
    Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFS). For demonstration purpose.
    rda| rds
    GRanges
  15. consensusSeekeR::NOrMAL_nucleosome_positions
    Nucleosome positions detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
    rda| rds
    GRanges
  16. consensusSeekeR::NOrMAL_nucleosome_ranges
    Ranges associated to nucleosomes detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
    rda| rds
    GRanges
  17. consensusSeekeR::NucPosSimulator_nucleosome_positions
    Nucleosome positions detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
    rda| rds
    GRanges
  18. consensusSeekeR::NucPosSimulator_nucleosome_ranges
    Ranges associated to nucleosomes detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
    rda| rds
    GRanges
  19. consensusSeekeR::PING_nucleosome_positions
    Nucleosome positions detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.
    rda| rds
    GRanges
  20. consensusSeekeR::PING_nucleosome_ranges
    Ranges associated to nucleosomes detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.
    rda| rds
    GRanges
  21. enrichViewNet::demoGOST
    The result of a functional enrichment analysis done with 'gprofiler2' (<https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html>).
    json| rda| rds
    list
  22. enrichViewNet::parentalNapaVsDMSODEG
    The result of a differential expression analysis done between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hours with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|24184 x 4
  23. enrichViewNet::parentalNapaVsDMSOEnrichment
    The result of an enrichment analysis has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
    json| rda| rds
    list
  24. enrichViewNet::rosaNapaVsDMSODEG
    The result of a differential expression analysis done between napabucasin treated and DMSO control MiaPaCa2 cells stably expressing the Rosa26 control vector. The cells were treated for 2 hours with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|23542 x 4
  25. enrichViewNet::rosaNapaVsDMSOEnrichment
    The result of an enrichment analysis that has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control MiaPaCa2 cells stably expressing the Rosa26 control vector. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
    json| rda| rds
    list
  26. methylInheritance::demoForTransgenerationalAnalysis
    The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
    json| rda| rds
    list
  27. methylInheritance::methylInheritanceResults
    All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
    rda| rds
    methylInheritanceAllResults
  28. methylInheritance::samplesForTransgenerationalAnalysis
    All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).
    json| rda| rds
    list
  29. RJMCMCNucleosomes::RJMCMC_result
    Nucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).
    rda| rds
    rjmcmcNucleosomes
  30. RJMCMCNucleosomes::reads_demo_01
    Forward reads and reverse reads in 'GRanges' format (for demo purpose).
    rda| rds
    GRanges
  31. RJMCMCNucleosomes::reads_demo_02
    Forward reads and reverse reads in 'GRanges' format (for demo purpose).
    rda| rds
    GRanges
  32. RJMCMCNucleosomes::syntheticNucleosomeReads
    Simulated dataset of reads generated by 'nucleoSim' package (for demo purpose).
    rda| rds
    syntheticNucReads
  33. similaRpeak::chr7Profiles
    ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)
    csv| json| rda| rds
    list
  34. similaRpeak::demoProfiles
    ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)
    csv| json| rda| rds
    list