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AlphaBeta

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


Bioconductor version: Release (3.18)

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 "4.3") and enter:


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

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")
AlphaBeta PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, Software
Version 1.16.0
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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Package Archives

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

Source Package AlphaBeta_1.16.0.tar.gz
Windows Binary AlphaBeta_1.16.0.zip
macOS Binary (x86_64) AlphaBeta_1.16.0.tgz
macOS Binary (arm64) AlphaBeta_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/AlphaBeta
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AlphaBeta
Bioc Package Browser https://code.bioconductor.org/browse/AlphaBeta/
Package Short Url https://bioconductor.org/packages/AlphaBeta/
Package Downloads Report Download Stats