BioTransition/DESCRIPTION at main · SolvingLab/BioTransition · GitHub

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Package: BioTransition
Type: Package
Title: Dynamic Network Biomarker Analysis for Critical Transitions
Version: 2.0.0
Date: 2026-01-23
Authors@R: c(
    person("Zaoqu", "Liu",
        email = "liuzaoqu@163.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-0452-742X")),
    person("Chuhan", "Zhang",
        role = "ctb",
        comment = "MDNB implementation"))
Description: A comprehensive toolkit for detecting critical transitions and
    identifying dynamic network biomarkers (DNB) in biological systems.
    Critical transitions, characterized by sudden shifts between distinct
    states, are prevalent in complex biological processes including disease
    progression, cellular differentiation, and developmental transitions.
    This package implements seven complementary DNB methodologies:
    (1) conventional DNB (cDNB) based on the original DNB theory
    (Chen et al. 2012 <doi:10.1038/srep00342>);
    (2) topological DNB (tDNB), a novel approach utilizing network topology
    and scale-free properties;
    (3) landscape DNB (LDNB) for quantifying state transitions
    (Liu et al. 2019 <doi:10.1093/nsr/nwy162>);
    (4) local DNB (LcDNB) leveraging protein-protein interaction networks;
    (5) module-based DNB (MDNB) for modular analysis
    (Li et al. 2022 <doi:10.1016/j.xinn.2022.100364>);
    (6) time-series network module biomarker (TSNMB) for temporal dynamics
    (Zhong et al. 2022 <doi:10.1093/jmcb/mjac052>);
    and (7) time-series leading edge (TSLE) analysis
    (Liu et al. 2020 <doi:10.1093/bioinformatics/btz758>).
    Core computational routines are implemented in C++ via 'Rcpp' for
    optimal performance. Compatible with bulk RNA-seq, single-cell RNA-seq,
    and spatial transcriptomics data. Includes curated protein-protein
    interaction networks for human and mouse from the STRING database.
License: GPL (>= 3) + file LICENSE
URL: https://github.com/SolvingLab/BioTransition,
    https://zaoqu-liu.r-universe.dev/BioTransition
BugReports: https://github.com/SolvingLab/BioTransition/issues
biocViews:
    Software,
    StatisticalMethod,
    Network,
    SystemsBiology,
    GeneExpression,
    Transcriptomics,
    SingleCell,
    Spatial,
    BiomedicalInformatics,
    DifferentialExpression
Encoding: UTF-8
ByteCompile: true
LazyData: true
LazyDataCompression: xz
Depends: R (>= 4.4.0)
Imports:
    methods,
    stats,
    utils,
    future (>= 1.21.0),
    furrr,
    magrittr,
    purrr (>= 1.0.0),
    dplyr (>= 1.0.0),
    parallel,
    WGCNA,
    dendextend,
    ggplot2,
    Rcpp (>= 1.0.0)
LinkingTo: Rcpp
Suggests:
    testthat (>= 3.0.0),
    knitr,
    rmarkdown,
    BiocStyle,
    BiocCheck
VignetteBuilder: knitr
Config/testthat/edition: 3
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)