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 (3.24)
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("GenomAutomorphism")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.15.2 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0) |
| Imports | Biostrings, MultipleAlignment, BiocGenerics, BiocParallel, Seqinfo, 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_1.15.2.tar.gz |
| Windows Binary (x86_64) | GenomAutomorphism_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | GenomAutomorphism_1.15.2.tgz |
| macOS Binary (sonoma-arm64) | GenomAutomorphism_1.15.2.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 |