GenomicAlignments
This is the development version of GenomicAlignments; for the stable release version, see GenomicAlignments.
Representation and manipulation of short genomic alignments
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("GenomicAlignments")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| Video | |
| Video |
Details
| biocViews | Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software |
| Version | 1.47.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (11.5 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
| Suggests | ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle |
| Linking To | S4Vectors, IRanges |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicAlignments |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicAlignments |
| Package Short Url | https://bioconductor.org/packages/GenomicAlignments/ |
| Package Downloads Report | Download Stats |