GenomicAlignments
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GenomicAlignments.
Representation and manipulation of short genomic alignments
Bioconductor version: 3.9
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, Valerie Obenchain, Martin Morgan
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("GenomicAlignments")
):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
Reference Manual | ||
NEWS | Text | |
Reading from a BAM file - Part 1 | Video | |
Reading from a BAM file - Part 2 | Video |
Details
biocViews | Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software |
Version | 1.20.1 |
In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
License | Artistic-2.0 |
Depends | R (>= 2.10), methods, BiocGenerics(>= 0.15.3), S4Vectors(>= 0.19.11), IRanges(>= 2.15.12), GenomeInfoDb(>= 1.13.1), GenomicRanges(>= 1.33.4), SummarizedExperiment(>= 1.9.13), Biostrings(>= 2.47.6), Rsamtools(>= 1.31.2) |
Imports | methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel |
System Requirements | |
URL |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | GenomicAlignments_1.20.1.tar.gz |
Windows Binary | GenomicAlignments_1.20.1.zip |
Mac OS X 10.11 (El Capitan) | GenomicAlignments_1.20.1.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 |
Old Source Packages for BioC 3.9 | Source Archive |