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 (3.18)
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("AlphaBeta")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("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")| AlphaBeta | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, Software |
| Version | 1.15.0 |
| 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) |
| Linking To | |
| Suggests | knitr, rmarkdown |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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_1.15.0.tar.gz |
| Windows Binary | AlphaBeta_1.15.0.zip |
| macOS Binary (x86_64) | AlphaBeta_1.15.0.tgz |
| macOS Binary (arm64) | AlphaBeta_1.15.0.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 |