Package: MesKit
Type: Package
Title: A tool kit for dissecting cancer evolution from multi-region
        derived tumor biopsies via somatic alterations
Version: 1.20.0
Authors@R: c(
  person('Mengni', 'Liu',   email = "niinleslie@gmail.com", role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9938-9973')),
  person('Jianyu', 'Chen', email = 'chenjy327@mail2.sysu.edu.cn', role = c('aut', 'ctb'), comment = c(ORCID = '0000-0003-4491-9265')),
  person('Xin', 'Wang', email = 'wangx555@mail2.sysu.edu.cn', role = c('aut', 'ctb'), comment = c(ORCID = '0000-0002-6072-599X'))
  )
Description: MesKit provides commonly used analysis and visualization
        modules based on mutational data generated by multi-region
        sequencing (MRS). This package allows to depict mutational
        profiles, measure heterogeneity within or between tumors from
        the same patient, track evolutionary dynamics, as well as
        characterize mutational patterns on different levels. Shiny
        application was also developed for a need of GUI-based
        analysis. As a handy tool, MesKit can facilitate the
        interpretation of tumor heterogeneity and the understanding of
        evolutionary relationship between regions in MRS study.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape
        (>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges,
        circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3),
        ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>=
        1.4.0), org.Hs.eg.db, clusterProfiler,
        TxDb.Hsapiens.UCSC.hg19.knownGene
Config/pak/sysreqs: libglpk-dev libicu-dev libpng-dev libxml2-dev
        libssl-dev perl zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:01:00 UTC
RemoteUrl: https://github.com/bioc/MesKit
RemoteRef: RELEASE_3_22
RemoteSha: 8a343152d19842154d089ceff9222284a8b52d87
NeedsCompilation: no
Packaged: 2026-03-05 08:15:43 UTC; root
Author: Mengni Liu [aut, cre] (ORCID: <https://orcid.org/0000-0001-9938-9973>),
  Jianyu Chen [aut, ctb] (ORCID: <https://orcid.org/0000-0003-4491-9265>),
  Xin Wang [aut, ctb] (ORCID: <https://orcid.org/0000-0002-6072-599X>)
Maintainer: Mengni Liu <niinleslie@gmail.com>
Built: R 4.5.2; ; 2026-03-05 08:19:14 UTC; windows
