DOI: 10.18129/B9.bioc.AlphaBeta  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see AlphaBeta.

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

Bioconductor version: 3.17

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>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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



PDF R Script AlphaBeta
PDF   Reference Manual
Text   NEWS


biocViews Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, Software
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 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)
Suggests knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package AlphaBeta_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) AlphaBeta_1.14.0.tgz
macOS Binary (arm64) AlphaBeta_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: