GenomicAlignments
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see GenomicAlignments.
Representation and manipulation of short genomic alignments
Bioconductor version: 3.7
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 "3.5") 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, Infrastructure, RNASeq, SNP, Sequencing, Software |
Version | 1.16.0 |
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(>= 0.17.28), IRanges(>= 2.13.25), GenomeInfoDb(>= 1.13.1), GenomicRanges(>= 1.31.19), 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_1.16.0.tar.gz |
Windows Binary | GenomicAlignments_1.16.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | GenomicAlignments_1.16.0.tgz |
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 |
Old Source Packages for BioC 3.7 | Source Archive |