GenomAutomorphism

DOI: 10.18129/B9.bioc.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 (3.17)

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>

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

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("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
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Details

biocViews ComparativeGenomics, FunctionalGenomics, MathematicalBiology, MultipleSequenceAlignment, Software
Version 1.1.1
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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
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
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Build Report  

Package Archives

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

Source Package GenomAutomorphism_1.1.1.tar.gz
Windows Binary
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/GenomAutomorphism/
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