DESCRIPTION

Package: AlphaBeta
Type: Package
Title: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
Version: 1.9.0
Authors@R: c(
    person("Yadollah", "Shahryary Dizaji", email = "shahryary@gmail.com", role = c("cre","aut")),
    person("Frank", "Johannes", email = "frank@jlab.org", role = "aut"),
    person("Rashmi", "Hazarika", email = "hazarika.rr@gmail.com", role = "aut"))
Description: AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants.
        The method has been specifically designed to:
        1. analyze 'germline' epimutations in the context of multi-generational mutation accumulation lines (MA-lines).
        2. analyze 'somatic' epimutations in the context of plant development and aging.
License: GPL-3
Depends:
    R (>= 3.6.0)
Imports:
    dplyr (>= 0.7),
    data.table (>= 1.10),
    stringr (>= 1.3),
    utils (>= 3.6.0),
    gtools (>= 3.8.0),
    optimx (>= 2018-7.10),
    expm (>= 0.999-4),
    stats (>= 3.6),
    BiocParallel (>= 1.18),
    igraph (>= 1.2.4),
    graphics (>= 3.6),
    ggplot2 (>= 3.2),
    grDevices (>= 3.6),
    plotly (>= 4.9)
Encoding: UTF-8
LazyData: false
LazyLoad: yes
VignetteBuilder: knitr
RoxygenNote: 7.1.0
Suggests: knitr,
    rmarkdown
biocViews: Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology