AlphaBeta

This package is for version 3.14 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: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, Software

Version 1.8.0

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)

System Requirements

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Package Archives

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

Source Package AlphaBeta_1.8.0.tar.gz

Windows Binary AlphaBeta_1.8.0.zip

macOS 10.13 (High Sierra) AlphaBeta_1.8.0.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

Old Source Packages for BioC 3.14 Source Archive