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Bioconductor - AlphaBeta (development version)

AlphaBeta

This is the development version of AlphaBeta; for the stable release version, see AlphaBeta.

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Bioconductor version: Development (3.22)

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.

Author: Yadollah Shahryary Dizaji [cre, aut], Frank Johannes [aut], Rashmi Hazarika [aut]

Maintainer: Yadollah Shahryary Dizaji <shahryary at gmail.com>

Citation (from within R, enter citation("AlphaBeta")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("AlphaBeta")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("AlphaBeta")
Details biocViews Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, Software Version 1.23.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 years) 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) System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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