GenomicAlignments
This is the released version of GenomicAlignments; for the devel version, see GenomicAlignments.
Representation and manipulation of short genomic alignments
Bioconductor version: Release (3.23)
Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
Author: Hervé Pagès [aut, cre], Valerie Obenchain [aut], Martin Morgan [aut], Fedor Bezrukov [ctb], Robert Castelo [ctb], Halimat C. Atanda [ctb] (Translated 'WorkingWithAlignedNucleotides' vignette from Sweave to RMarkdown / HTML.)
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("GenomicAlignments")):
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("GenomicAlignments")
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("GenomicAlignments")| An Introduction to the GenomicAlignments Package | R Script | |
| Counting reads with summarizeOverlaps | R Script | |
| Overlap encodings | R Script | |
| Working with aligned nucleotides (WORK-IN-PROGRESS!) | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| - YouTube | Video | |
| - YouTube | Video |
Details
| biocViews | Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.47.6), IRanges(>= 2.23.9), Seqinfo, GenomicRanges(>= 1.61.1), SummarizedExperiment(>= 1.39.1), Biostrings(>= 2.77.2), Rsamtools(>= 2.25.1) |
| Imports | methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel, cigarillo(>= 0.99.2) |
| System Requirements | |
| URL | https://bioconductor.org/packages/GenomicAlignments |
| Bug Reports | https://github.com/Bioconductor/GenomicAlignments/issues |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicAlignments_1.48.0.tar.gz |
| Windows Binary (x86_64) | GenomicAlignments_1.48.0.zip |
| macOS Binary (big-sur-x86_64) | GenomicAlignments_1.48.0.tgz |
| macOS Binary (sonoma-arm64) | GenomicAlignments_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicAlignments |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicAlignments |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicAlignments/ |
| Package Short Url | https://bioconductor.org/packages/GenomicAlignments/ |
| Package Downloads Report | Download Stats |