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

Bioconductor version: Release (3.19)

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")):


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AlphaBeta PDF R Script
Reference Manual PDF


biocViews Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, Software
Version 1.18.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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)
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Source Package AlphaBeta_1.18.0.tar.gz
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