DESCRIPTION

Package: KINNET
Type: Package
Title: Kinase INteraction NETwork Generation
Version: 0.4.0.9002
Authors@R: c(
    person(given = c("Ali", "Sajid"),
           family = "Imami",
           role = c("aut", "cre"),
           email = "Ali.Sajid.Imami@gmail.com",
           comment = c(ORCID = "0000-0003-3684-3539")),
    person(given = "Khaled",
           family = "Alganem",
           role = c("aut"),
           email = "Khaled.Alganem@rockets.utoledo.edu",
           comment = c(ORCID = "0000-0003-3234-7669")),
    person(given = c("Justin", "Fortune"),
           family = "Creeden",
           role = c("aut"),
           email = "Justin.Creeden@rockets.utoledo.edu",
           comment = c(ORCID = "0000-0003-3123-8401")),
    person(given = "Alex",
           family = "Joyce",
           role = c("aut"),
           email = "Alex.Joyce2@rockets.utoledo.edu",
           comment = c(ORCID = "0000-0003-0303-2481")))
Description: This package provides the functionality to process PamGene's PamChip
    Data Output and generate kinase interaction networks from that.
    This project uses a bayesian algorithm to generate bayesian networks for
     defining dependence relationships between peptide sequences in the PamChip data.
     It then uses a novel kinase assignment method to assign upstream kinases to each 
     peptide which is then output as a graph.
License: GPL (>= 3) | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: 
    methods,
    readr,
    dplyr,
    tibble,
    bnlearn,
    stringr,
    tidyselect,
    purrr,
    tidyr,
    Rgraphviz,
    graph,
    rlang,
    effectsize
Depends: 
    R (>= 2.10)
RoxygenNote: 7.1.1
Collate: 
    'assign_kinases.R'
    'compare_kinased_graphs.R'
    'distances.R'
    'equalize_kinase_graphs.R'
    'filter_peptides.R'
    'make_model.R'
    'pamchip_data.R'
    'pamchip_data_ptk.R'
    'pamchip_data_stk.R'
    'probability_matrix.R'
    'ptk_methods.R'
    'render_kinased_graph.R'
    'render_reduced_kinased_graph.R'
    'stk_methods.R'
    'subset_data.R'
    'update_probability_matrix.R'
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3