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 (3.21)
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] (ORCID:
Maintainer: Robersy Sanchez <genomicmath at gmail.com>
citation("GenomAutomorphism")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics, FunctionalGenomics, MathematicalBiology, MultipleSequenceAlignment, Software, WholeGenome |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, matrixStats, XVector, 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 |
See More
| Suggests | spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomAutomorphism_1.9.0.tar.gz |
| Windows Binary (x86_64) | GenomAutomorphism_1.9.0.zip |
| macOS Binary (x86_64) | GenomAutomorphism_1.9.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomAutomorphism |
| Source Repository (Developer Access) | git clone [email protected]:packages/GenomAutomorphism |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomAutomorphism/ |
| Package Short Url | https://bioconductor.org/packages/GenomAutomorphism/ |
| Package Downloads Report | Download Stats |