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  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::association_mutations
    List providing mutations as binary variables and signatures assignments for 656 breast cancer patients
    json| rda| rds
    list
  6. RESOLVE::association_survival
    List providing clinical data and signatures assignments for 359 pancreatic cancer patients
    json| rda| rds
    list
  7. RESOLVE::background
    Germline replication error
    json| rda| rds
    numeric
  8. RESOLVE::background2
    COSMIC replication error
    json| rda| rds
    numeric
  9. 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
  10. 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
  11. RESOLVE::patients
    Point mutations for 560 breast tumors
    csv| json| rda| rds
    matrix|560 x 96
  12. RESOLVE::plot_data_examples
    List data structure to run examples
    json| rda| rds
    list
  13. RESOLVE::sbs_assignments
    SBS assignments for 560 breast tumors
    json| rda| rds
    list
  14. 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
  15. SparseSignatures::background
    germline replication error
    json| rda| rds
    numeric
  16. SparseSignatures::background2
    COSMIC replication error
    json| rda| rds
    numeric
  17. 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
  18. SparseSignatures::imported_data
    example of imported data from Nik-Zainal, Serena, et al. (2016).
    csv| json| rda| rds
    matrix|3 x 96
  19. SparseSignatures::lambda_range_example
    example of results obtained with the function lambdaRangeBetaEvaluation on the counts input from Nik-Zainal, Serena, et al. (2016).
    json| rda| rds
    matrix|1 x 7
  20. SparseSignatures::mutation_categories
    trinucleotides mutation categories
    csv| xlsx| json| ndjson| rda| rds
    data.table|96 x 3
  21. 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
  22. SparseSignatures::patients
    point mutations for 560 breast tumors
    csv| json| rda| rds
    matrix|560 x 96
  23. 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
  24. 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