Package: jellyfisher
Title: Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots
Version: 1.1.2
Authors@R: 
    person("Kari", "Lavikka", , "kari@karilavikka.fi", role = c("cph", "aut", "cre"),
           comment = c(ORCID = "0000-0002-4163-4945"))
Description: Generates interactive Jellyfish plots to visualize
        spatiotemporal tumor evolution by integrating sample and
        phylogenetic trees into a unified plot. This approach provides
        an intuitive way to analyze tumor heterogeneity and evolution
        over time and across anatomical locations. The Jellyfish plot
        visualization design was first introduced by Lahtinen, Lavikka,
        et al. (2023, <doi:10.1016/j.ccell.2023.04.017>). This package
        also supports visualizing ClonEvol results, a tool developed by
        Dang, et al. (2017, <doi:10.1093/annonc/mdx517>), for analyzing
        clonal evolution from multi-sample sequencing data. The
        'clonevol' package is not available on CRAN but can be
        installed from its GitHub repository
        (<https://github.com/hdng/clonevol>).
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
LazyData: true
URL: https://github.com/HautaniemiLab/jellyfisher,
        https://hautaniemilab.github.io/jellyfisher/
BugReports: https://github.com/HautaniemiLab/jellyfisher/issues
Imports: htmlwidgets, dplyr, stringr
Suggests: knitr, rmarkdown, clonevol, testthat (>= 3.0.0)
Depends: R (>= 4.1.0)
VignetteBuilder: knitr
biocViews: Visualization, Phylogenetics, Software, Spatial
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev
Repository: https://hautaniemilab.r-universe.dev
Date/Publication: 2026-08-21 06:32:25 UTC
RemoteUrl: https://github.com/hautaniemilab/jellyfisher
RemoteRef: HEAD
RemoteSha: f54ff34e541685c8cb94710c48cc2ce1df738845
NeedsCompilation: no
Packaged: 2026-10-20 08:29:18 UTC; root
Author: Kari Lavikka [cph, aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4163-4945>)
Maintainer: Kari Lavikka <kari@karilavikka.fi>