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GenomAutomorphism

This is the development version of GenomAutomorphism; for the stable release version, see GenomAutomorphism.

Compute the automorphisms between DNA's Abelian group representations


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("GenomAutomorphism")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews ComparativeGenomics, FunctionalGenomics, MathematicalBiology, MultipleSequenceAlignment, Software
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements
URL https://github.com/genomaths/GenomAutomorphism
Bug Reports https://github.com/genomaths/GenomAutomorphism/issues
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Suggests spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr
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Package Archives

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

Source Package GenomAutomorphism_1.5.0.tar.gz
Windows Binary GenomAutomorphism_1.5.0.zip
macOS Binary (x86_64) GenomAutomorphism_1.5.0.tgz
macOS Binary (arm64)
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/
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