AlphaBeta
This is thereleased version of AlphaBeta; for the devel version, seeAlphaBeta.
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("AlphaBeta")For older versions of R, please refer to the appropriateBioconductor 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 | 1.24.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 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 | |
| URL |
See More
| Suggests | knitr,rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | AlphaBeta_1.24.0.tar.gz |
| Windows Binary (x86_64) | AlphaBeta_1.24.0.zip |
| macOS Binary (x86_64) | AlphaBeta_1.24.0.tgz |
| macOS Binary (arm64) | AlphaBeta_1.24.0.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 |