Biostrings
This is the released version of Biostrings; for the devel version, see Biostrings.
Efficient manipulation of biological strings
Bioconductor version: Release (3.23)
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Author: Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Robert Gentleman [aut], Saikat DebRoy [aut], Vince Carey [ctb], Nicolas Delhomme [ctb], Felix Ernst [ctb], Wolfgang Huber [ctb] ('matchprobes' vignette), Beryl Kanali [ctb] (Converted 'MultipleAlignments' vignette from Sweave to RMarkdown), Haleema Khan [ctb] (Converted 'matchprobes' vignette from Sweave to RMarkdown), Aidan Lakshman [ctb], Kieran O'Neill [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Albert Vill [ctb], Jen Wokaty [ctb] (Converted 'matchprobes' vignette from Sweave to RMarkdown), Erik Wright [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("Biostrings")):
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")
BiocManager::install("Biostrings")
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("Biostrings")| A short presentation of the basic classes defined in Biostrings 2 | R Script | |
| Biostrings Quick Overview | ||
| Handling probe sequence information | HTML | R Script |
| Multiple Alignments | HTML | R Script |
| Pairwise Sequence Alignments | ||
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software |
| Version | 2.80.1 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.31.2), XVector(>= 0.37.1), Seqinfo |
| Imports | methods, grDevices, stats, crayon |
| System Requirements | |
| URL | https://bioconductor.org/packages/Biostrings |
| Bug Reports | https://github.com/Bioconductor/Biostrings/issues |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Biostrings_2.80.1.tar.gz |
| Windows Binary (x86_64) | Biostrings_2.80.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Biostrings_2.80.1.tgz |
| macOS Binary (sonoma-arm64) | Biostrings_2.80.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Biostrings |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Biostrings |
| Bioc Package Browser | https://code.bioconductor.org/browse/Biostrings/ |
| Package Short Url | https://bioconductor.org/packages/Biostrings/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |