Package: transomics2cytoscape
Title: A tool set for 3D Trans-Omic network visualization with
        Cytoscape
Version: 1.21.0
Authors@R: c(
    person ("Kozo", "Nishida", email = "kozo.nishida@gmail.com",
        role = c("aut", "cre"), comment = c(ORCID = "0000-0001-8501-7319")),
    person ("Katsuyuki", "Yugi", email = "katsuyuki.yugi@riken.jp",
        role = c("aut"), comment = c(ORCID = "0000-0002-2046-4289"))
    )
Description: transomics2cytoscape generates a file for 3D transomics
        visualization by providing input that specifies the IDs of
        multiple KEGG pathway layers, their corresponding Z-axis
        heights, and an input that represents the edges between the
        pathway layers. The edges are used, for example, to describe
        the relationships between kinase on a pathway and enzyme on
        another pathway. This package automates creation of a
        transomics network as shown in the figure in Yugi.2014
        (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape
        automation (https://doi.org/10.1186/s13059-019-1758-4).
License: Artistic-2.0
Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown
Encoding: UTF-8
biocViews: Network, Software, Pathways, DataImport, KEGG
VignetteBuilder: knitr
SystemRequirements: Cytoscape >= 3.10.0
RoxygenNote: 7.1.2
Config/pak/sysreqs: make libicu-dev libpng-dev libxml2-dev libssl-dev
        python3 libzmq3-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:01:08 UTC
RemoteUrl: https://github.com/bioc/transomics2cytoscape
RemoteRef: HEAD
RemoteSha: ec6e45e93f4bd3b869c49ec25e3a89829acc3241
NeedsCompilation: no
Packaged: 2026-02-27 08:30:46 UTC; root
Author: Kozo Nishida [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8501-7319>),
  Katsuyuki Yugi [aut] (ORCID: <https://orcid.org/0000-0002-2046-4289>)
Maintainer: Kozo Nishida <kozo.nishida@gmail.com>
Built: R 4.6.0; ; 2026-02-27 08:32:23 UTC; unix
