Package: AlphaBeta
Type: Package
Title: Computational inference of epimutation rates and spectra from
        high-throughput DNA methylation data in plants
Version: 1.25.0
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
LazyLoad: yes
VignetteBuilder: knitr
RoxygenNote: 7.1.0
Suggests: knitr, rmarkdown
biocViews: Epigenetics, FunctionalGenomics, Genetics,
        MathematicalBiology
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libxml2-dev
        libssl-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:53:31 UTC
RemoteUrl: https://github.com/bioc/AlphaBeta
RemoteRef: HEAD
RemoteSha: 26028388eb49b16f8ddcc37e5184d9216814675e
NeedsCompilation: no
Packaged: 2026-01-28 08:04:40 UTC; root
Author: Yadollah Shahryary Dizaji [cre, aut],
  Frank Johannes [aut],
  Rashmi Hazarika [aut]
Maintainer: Yadollah Shahryary Dizaji <shahryary@gmail.com>
Built: R 4.6.0; ; 2026-01-28 08:07:21 UTC; windows
