MultipleAlignment
This is the development version of MultipleAlignment; to use it, please install the devel version of Bioconductor.
Representation of multiple sequence alignments in Bioconductor
Bioconductor version: Development (3.24)
The package implements a set of S4 classes (DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment) for representing Multiple Sequence Alignments (MSA). The classes allow users to represent groups of aligned DNA, RNA or amino acid sequences as a single object. The package also provides functions to read/write such object from/to traditional MSA file formats including Stockholm and Clustal.
Author: Marc Carlson [aut], Patrick Aboyoun [aut], Hervé Pagès [cre]
, Beryl Kanali [ctb] (Converted 'MultipleAlignments' vignette from Sweave to RMarkdown), Michael Lawrence [ctb], Martin Morgan [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("MultipleAlignment")):
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("MultipleAlignment")
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("MultipleAlignment")| Multiple Alignments | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, MultipleSequenceAlignment, Software |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | BiocGenerics(>= 0.59.10), S4Vectors, IRanges, Seqinfo, Biostrings |
| Imports | methods, stats |
| System Requirements | |
| URL | https://bioconductor.org/packages/MultipleAlignment |
| Bug Reports | https://github.com/Bioconductor/MultipleAlignment/issues |
See More
| Suggests | pwalign, testthat, knitr, rmarkdown, BiocStyle |
| 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 | MultipleAlignment_0.99.5.tar.gz |
| Windows Binary (x86_64) | MultipleAlignment_0.99.5.zip |
| macOS Binary (big-sur-x86_64) | MultipleAlignment_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | MultipleAlignment_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MultipleAlignment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MultipleAlignment |
| Bioc Package Browser | https://code.bioconductor.org/browse/MultipleAlignment/ |
| Package Short Url | https://bioconductor.org/packages/MultipleAlignment/ |
| Package Downloads Report | Download Stats |