Package: MesKit
Type: Package
Title: A tool kit for dissecting cancer evolution from multi-region
        derived tumor biopsies via somatic alterations
Version: 1.4.0
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
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: RELEASE_3_14
git_last_commit: 0782512
git_last_commit_date: 2021-10-26
Date/Publication: 2021-10-26
NeedsCompilation: no
Packaged: 2021-10-26 21:51:02 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 4.1.1; ; 2021-11-05 13:20:00 UTC; unix
