1. OncoScore::genes
    A list of genes
    json| rda| rds
    character
  2. OncoScore::query
    The result of perform.web.query on genes
    csv| json| rda| rds
    matrix|5 x 2
  3. OncoScore::query.timepoints
    The result of perform.time.series.query on genes and timepoints
    csv| json| rda| rds
    list
  4. OncoScore::timepoints
    A list of timepoints
    json| rda| rds
    character
  5. RESOLVE::background
    Germline replication error
    json| rda| rds
    numeric
  6. RESOLVE::background2
    COSMIC replication error
    json| rda| rds
    numeric
  7. RESOLVE::cn_example_reduced
    A reduced version of the copy number data for 5 TCGA samples in the format compatible with the import function
    csv| xlsx| json| ndjson| rda| rds
    data.frame|353 x 6
  8. RESOLVE::id_example_reduced
    A reduced version of the indel data for 3 samples in the format compatible with the import function
    csv| xlsx| json| ndjson| rda| rds
    data.frame|489 x 6
  9. RESOLVE::patients
    Point mutations for 560 breast tumors
    csv| json| rda| rds
    matrix|560 x 96
  10. RESOLVE::plot_data_examples
    List data structure to run examples
    json| rda| rds
    list
  11. RESOLVE::ssm560_reduced
    A reduced version of the point mutations for 560 breast tumors in the format compatible with the import function
    csv| xlsx| json| ndjson| rda| rds
    data.table|22828 x 6
  12. SIMLR::BuettnerFlorian
    test dataset for SIMLR
    rda| rds
    list
  13. SIMLR::ZeiselAmit
    test dataset for SIMLR large scale
    rda| rds
    list
  14. SparseSignatures::background
    germline replication error
    json| rda| rds
    numeric
  15. SparseSignatures::background2
    COSMIC replication error
    json| rda| rds
    numeric
  16. SparseSignatures::cv_example
    example of results obtained with the function nmf.LassoCV on the counts input from Nik-Zainal, Serena, et al. (2016).
    json| rda| rds
    list
  17. SparseSignatures::imported_data
    example of imported data from Nik-Zainal, Serena, et al. (2016).
    csv| json| rda| rds
    matrix|3 x 96
  18. SparseSignatures::lambda_range_example
    example of results obtained with the function evaluate.lambda.range on the counts input from Nik-Zainal, Serena, et al. (2016).
    json| rda| rds
    matrix|1 x 7
  19. SparseSignatures::mutation_categories
    trinucleotides mutation categories
    csv| xlsx| json| ndjson| rda| rds
    data.table|96 x 3
  20. SparseSignatures::nmf_LassoK_example
    example of results obtained with the function nmf.LassoK on the counts input from Nik-Zainal, Serena, et al. (2016).
    json| rda| rds
    list
  21. SparseSignatures::patients
    point mutations for 560 breast tumors
    csv| json| rda| rds
    matrix|560 x 96
  22. SparseSignatures::ssm560_reduced
    a reduced version of the point mutations for 560 breast tumors in the format compatible with the import function
    csv| xlsx| json| ndjson| rda| rds
    data.table|22828 x 6
  23. SparseSignatures::starting_betas_example
    example of results obtained with the function starting.betas.estimation on the counts input from Nik-Zainal, Serena, et al. (2016).
    csv| json| rda| rds
    matrix|10 x 1
  24. TRONCO::aCML
    Atypical chronic myeloid leukemia dataset
    json| rda| rds
    list
  25. TRONCO::crc_gistic
    GISTIC example data
    csv| json| rda| rds
    matrix|9 x 6
  26. TRONCO::crc_maf
    MAF example data
    csv| xlsx| json| ndjson| rda| rds
    data.frame|17 x 55
  27. TRONCO::crc_plain
    Plain mutation dataset
    csv| xlsx| json| ndjson| rda| rds
    data.frame|5 x 6
  28. TRONCO::maf
    MAF example data
    csv| xlsx| json| ndjson| rda| rds
    data.frame|16 x 66
  29. TRONCO::muts
    Simple mutation dataset
    json| rda| rds
    list
  30. TRONCO::stage
    Stage information for test_dataset
    csv| xlsx| json| ndjson| rda| rds
    data.frame|40 x 1
  31. TRONCO::test_dataset
    A complete dataset with hypotheses
    json| rda| rds
    list
  32. TRONCO::test_dataset_no_hypos
    A complete dataset
    json| rda| rds
    list
  33. TRONCO::test_model
    A complete dataset with a reconstructed model
    rda| rds
    list
  34. TRONCO::test_model_kfold
    A complete dataset with a reconstructed model and crossvalidation informations
    rda| rds
    list