1. CITMIC::CITMIC_Data
    An environment variable that includes some example data
    rda| rds
    environment
  2. DrugSim2DR::myenv
    An environment variable which includes some example data
    rda| rds
    environment
  3. DRviaSPCN::envData
    An environment variable which includes some example data
    rda| rds
    environment
  4. DTSEA::example_disease_list
    An example vector of disease nodes
    json| rda| rds
    character
  5. DTSEA::example_drug_target_list
    An example data frame of drug target lists
    csv| xlsx| json| ndjson| rda| rds
    data.frame|252 x 3
  6. DTSEA::example_ppi
    An example human gene functional interaction network object
    rda| rds
    igraph
  7. DTSEA::random_graph
    A random graph for the computation of the separation measure
    rda| rds
    igraph
  8. ICDS::envData
    The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
    rda| rds
    environment
  9. IDMIR::MirnaData
    An environment variable that includes some example data
    rda| rds
    environment
  10. iPRISM::Seeds
    Seed Node Names
    json| rda| rds
    character
  11. iPRISM::data.cell
    data.cell
    csv| json| rda| rds
    matrix|121 x 21
  12. iPRISM::data.path
    data.path
    csv| json| rda| rds
    matrix|121 x 17
  13. iPRISM::data_sig
    data_sig
    csv| json| rda| rds
    matrix|121 x 31
  14. iPRISM::genelist_cp
    TME gene list after random walks
    json| rda| rds
    numeric
  15. iPRISM::genelist_hla
    HLA gene list after random walks
    json| rda| rds
    numeric
  16. iPRISM::genelist_imm
    ICI gene list after random walks
    json| rda| rds
    numeric
  17. iPRISM::path_list
    path_list
    json| rda| rds
    list
  18. iPRISM::ppi
    A protein-protein physical interaction network (PPI network)
    rda| rds
    igraph
  19. iPRISM::pred_value
    Original Class Labels for Samples
    json| rda| rds
    character
  20. LncPath::LncPathEnvir
    The variables in the environment variable 'LncPathEnvir' of the system
    rda| rds
    environment
  21. MiRSEA::envData
    The variables in the environment include predefine pathway, target information of miRNAs,an expression profile and a example result of miRNA list
    rda| rds
    environment
  22. pathwayTMB::PTMB_matrix
    PTMB_matrix, the Pathway-based Tumor Mutational Burden matrix
    csv| xlsx| json| ndjson| rda| rds
    data.frame|27 x 35
  23. pathwayTMB::final_character
    final_character, the example's final signature
    json| rda| rds
    character
  24. pathwayTMB::gene_path
    gene_path, the pathways geneset
    json| rda| rds
    list
  25. pathwayTMB::genesmbol
    genesmbol, the coding genes' length
    csv| json| rda| rds
    list
  26. pathwayTMB::mut_matrix
    mut_matrix, mutations matrix
    csv| json| rda| rds
    matrix|673 x 35
  27. pathwayTMB::sur
    sur, the samples' survival data
    csv| xlsx| json| ndjson| rda| rds
    data.frame|110 x 2
  28. PMAPscore::final_signature
    final_signature, the final prognosis-related pathways
    json| rda| rds
    character
  29. PMAPscore::gene_Ucox
    gene_Ucox
    csv| xlsx| json| ndjson| rda| rds
    data.frame|4287 x 5
  30. PMAPscore::gene_Ucox_res
    gene_Ucox_res, the univariate Cox regression result of candidate genes.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|4287 x 5
  31. PMAPscore::gene_symbol_Entrez
    gene_symbol_Entrez, the genes' symbol and ENTREZID
    csv| xlsx| json| ndjson| rda| rds
    data.frame|54245 x 2
  32. PMAPscore::km_data
    km_data
    csv| xlsx| json| ndjson| rda| rds
    data.frame|105 x 10
  33. PMAPscore::maf_data
    maf_data
    csv| xlsx| json| ndjson| rda| rds
    data.frame|24461 x 4
  34. PMAPscore::maffile
    maffile
    rda| rds
    MAF
  35. PMAPscore::mut_num
    mut_num
    csv| json| rda| rds
    matrix|13858 x 105
  36. PMAPscore::mut_sam
    mut_sam
    csv| json| rda| rds
    matrix|13858 x 2
  37. PMAPscore::mut_sample
    mut_sample
    csv| json| rda| rds
    matrix|13858 x 2
  38. PMAPscore::mut_status
    mut_status
    csv| json| rda| rds
    matrix|13858 x 105
  39. PMAPscore::path_Ucox_mul
    path_Ucox_mul
    csv| json| rda| rds
    matrix|7 x 5
  40. PMAPscore::path_Ucox_mul_res
    path_Ucox_mul_res
    csv| json| rda| rds
    matrix|7 x 5
  41. PMAPscore::path_cox_data
    path_cox_data
    csv| xlsx| json| ndjson| rda| rds
    data.frame|105 x 9
  42. PMAPscore::path_gene
    path_gene
    json| rda| rds
    list
  43. PMAPscore::pfs_score
    pfs_score
    csv| json| rda| rds
    matrix|123 x 105
  44. PMAPscore::response
    response
    csv| xlsx| json| ndjson| rda| rds
    data.frame|110 x 2
  45. PMAPscore::roc_data
    roc_data, the data frame use for ploting ROC curve
    csv| json| rda| rds
    matrix|105 x 4
  46. PMAPscore::sig
    sig
    json| rda| rds
    character
  47. PMAPscore::sur
    sur
    csv| xlsx| json| ndjson| rda| rds
    data.frame|110 x 2
  48. PMAPscore::symbol_Entrez
    symbol_Entrez
    csv| xlsx| json| ndjson| rda| rds
    data.frame|54245 x 2
  49. ProgModule::candidate_module
    candidate_module, candidate module
    csv| json| rda| rds
    list
  50. ProgModule::final_candidate_module
    final_candidate_module, Final candidate modules
    json| rda| rds
    list
  51. ProgModule::local_network
    local_network, local network gene set
    json| rda| rds
    list
  52. ProgModule::maf_data
    maf_data, MAF file
    csv| xlsx| json| ndjson| rda| rds
    data.frame|3745 x 10
  53. ProgModule::module
    module, gene set
    json| rda| rds
    character
  54. ProgModule::mut_status
    mut_status, mutations matrix
    csv| json| rda| rds
    matrix|338 x 331
  55. ProgModule::net
    net, network
    rda| rds
    igraph
  56. ProgModule::plotMutInteract_moduledata
    plotMutInteract_moduledata
    json| rda| rds
    list
  57. ProgModule::plotMutInteract_mutdata
    plotMutInteract_mutdata
    csv| json| rda| rds
    matrix|89 x 430
  58. ProgModule::subnet
    subnet, network
    rda| rds
    igraph
  59. ProgModule::univarCox_result
    univarCox_result
    json| rda| rds
    numeric
  60. SMDIC::envData
    envData
    rda| rds
    environment
  61. SMDIC::xCell.data
    xCell datasets
    rda| rds
    list
  62. ssMutPA::Path_ES
    Path_ES Single-sample mutation-based pathway enrichment score profiles.
    csv| json| rda| rds
    matrix|215 x 882
  63. ssMutPA::Path_Name
    Path_Name
    json| rda| rds
    character
  64. ssMutPA::RWR_res
    RWR_res Random walk results based on mutated genes in a single sample.
    json| rda| rds
    numeric
  65. ssMutPA::Seeds_Score
    Seeds_Score The local weight of seed nodes.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|35 x 2
  66. ssMutPA::cox_data
    cox_data Univariate cox proportional hazards regression data.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|20 x 293
  67. ssMutPA::dot_data
    dot_data A data frame.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|350 x 4
  68. ssMutPA::mut_onco
    mut_onco A binary mutation matrix.
    csv| json| rda| rds
    matrix|11968 x 44
  69. ssMutPA::mut_status
    mut_status A binary mutation matrix.
    csv| json| rda| rds
    matrix|12802 x 50
  70. ssMutPA::samp_class_onco
    samp_class_onco
    json| rda| rds
    integer
  71. ssMutPA::sample_class
    sample_class The subtype labels of samples.
    json| rda| rds
    integer
  72. ssMutPA::sur_onco
    sur_onco
    csv| xlsx| json| ndjson| rda| rds
    data.frame|44 x 2
  73. SubtypeDrug::Colork
    Color
    json| rda| rds
    character
  74. SubtypeDrug::Disease_drugs
    Simulated result data
    json| rda| rds
    list
  75. SubtypeDrug::Drugs_CID
    Correspondence table of drug label and drug ID in PubCham database
    csv| xlsx| json| ndjson| rda| rds
    data.frame|1194 x 2
  76. SubtypeDrug::Geneexp
    Simulated gene expression data
    csv| json| rda| rds
    matrix|3000 x 40
  77. SubtypeDrug::GeneexpT
    Gene expression data for testing
    csv| json| rda| rds
    matrix|51 x 40
  78. SubtypeDrug::SpwNetworkData
    Subpathway network structure data
    rda| rds
    list
  79. SubtypeDrug::Subtype_drugs
    Simulation result data
    json| rda| rds
    list
  80. SubtypeDrug::UserDS
    Simulated user-defined drug regulator subpathway dataset
    csv| json| rda| rds
    list
  81. SubtypeDrug::UserDST
    User-defined drug regulator subpathway dataset for testing
    csv| json| rda| rds
    list
  82. SubtypeDrug::UserGS
    Simulated user-defined gene set data
    json| rda| rds
    list
  83. SubtypeDrug::UserGST
    User-defined gene set data for testing
    json| rda| rds
    list