AlphaBeta

DOI: 10.18129/B9.bioc.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 (3.11)

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 "4.0") and enter:

if (!requireNamespace("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")

 

PDF R Script AlphaBeta
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, Software
Version 1.1.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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)
LinkingTo
Suggests knitr, rmarkdown
SystemRequirements
Enhances
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Depends On Me
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Build Report  

Package Archives

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

Source Package AlphaBeta_1.1.0.tar.gz
Windows Binary AlphaBeta_1.1.0.zip
Mac OS X 10.11 (El Capitan) AlphaBeta_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/AlphaBeta
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AlphaBeta
Package Short Url https://bioconductor.org/packages/AlphaBeta/
Package Downloads Report Download Stats

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