Package: MesKit
Type: Package
Title: A tool kit for dissecting cancer evolution from multi-region
        derived tumor biopsies via somatic alterations
Version: 1.0.0
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 decipher ITH, infer metastatic routes as well as uncover the underlying process of mutagenesis. Shiny application was also developed for a need of GUI-based analysis.  As a handy tool, MesKit can facilitate the understanding of cancer cell evolution and its relevance to cancer therapeutics.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 4.0.0)
Imports: methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape,
        ggrepel, pracma, ggridges, circlize, cowplot, mclust, phangorn,
        ComplexHeatmap (>= 1.9.3), ggplot2, RColorBrewer, grDevices,
        stats, utils, S4Vectors
RoxygenNote: 7.1.1
Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>=
        1.4.0), org.Hs.eg.db, clusterProfiler
VignetteBuilder: knitr
biocViews: Software, SomaticMutation, GeneticVariability, Genetics,
        Classification, VariantAnnotation, DataRepresentation,
        Visualization, Sequencing, GUI
NeedsCompilation: no
BugReports: https://github.com/Niinleslie/MesKit/issues
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: RELEASE_3_12
git_last_commit: 3f41cb0
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-27
Packaged: 2020-10-28 01:28:54 UTC; biocbuild
Author: Mengni Liu [aut, cre] (<https://orcid.org/0000-0001-9938-9973>),
  Jianyu Chen [aut, ctb] (<https://orcid.org/0000-0003-4491-9265>),
  Xin Wang [aut, ctb] (<https://orcid.org/0000-0002-6072-599X>)
Maintainer: Mengni Liu <niinleslie@gmail.com>
Built: R 4.0.3; ; 2020-10-31 13:15:24 UTC; unix
