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
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
Repository: https://cogdisreslab.r-universe.dev
Date/Publication: 2022-01-14 16:32:11 UTC
RemoteUrl: https://github.com/CogDisResLab/KINNET
RemoteRef: HEAD
RemoteSha: 8c901f74fee88662aa6630dbe536ba08e7a7af54
NeedsCompilation: no
Packaged: 2026-07-06 06:08:22 UTC; root
Author: Ali Sajid Imami [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3684-3539>),
  Khaled Alganem [aut] (ORCID: <https://orcid.org/0000-0003-3234-7669>),
  Justin Fortune Creeden [aut] (ORCID:
    <https://orcid.org/0000-0003-3123-8401>),
  Alex Joyce [aut] (ORCID: <https://orcid.org/0000-0003-0303-2481>)
Maintainer: Ali Sajid Imami <Ali.Sajid.Imami@gmail.com>