Package: BioTransition
Type: Package
Title: Dynamic Network Biomarker Analysis for Critical Transitions
Version: 2.1.0
Date: 2026-06-15
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)
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-06-15 07:45:55 UTC
RemoteUrl: https://github.com/SolvingLab/BioTransition
RemoteRef: HEAD
RemoteSha: 665d96c2259e2f517811404ead2c233f23d079d0
NeedsCompilation: yes
Packaged: 2026-07-15 08:02:02 UTC; root
Author: Zaoqu Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-0452-742X>),
  Chuhan Zhang [ctb] (MDNB implementation)
Maintainer: Zaoqu Liu <liuzaoqu@163.com>