GenomAutomorphism

DOI: 10.18129/B9.bioc.GenomAutomorphism  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see GenomAutomorphism.

Compute the automorphisms between DNA's Abelian group representations

Bioconductor version: 3.17

This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.

Author: Robersy Sanchez [aut, cre]

Maintainer: Robersy Sanchez <genomicmath at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("GenomAutomorphism")

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("GenomAutomorphism")

 

HTML	R Script	Get started-with GenomAutomorphism
PDF		Reference Manual
Text		NEWS

Details

biocViews	ComparativeGenomics, FunctionalGenomics, MathematicalBiology, MultipleSequenceAlignment, Software
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.2)
Imports	Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils
LinkingTo
Suggests	spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr
SystemRequirements
Enhances
URL	https://github.com/genomaths/GenomAutomorphism
BugReports	https://github.com/genomaths/GenomAutomorphism/issues
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	GenomAutomorphism_1.2.0.tar.gz
Windows Binary	GenomAutomorphism_1.2.0.zip (64-bit only)
macOS Binary (x86_64)	GenomAutomorphism_1.2.0.tgz
macOS Binary (arm64)	GenomAutomorphism_1.1.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomAutomorphism
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomAutomorphism
Bioc Package Browser	https://code.bioconductor.org/browse/GenomAutomorphism/
Package Short Url	https://bioconductor.org/packages/GenomAutomorphism/
Package Downloads Report	Download Stats