To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicAlignments")

In most cases, you don't need to download the package archive at all.

GenomicAlignments

Representation and manipulation of short genomic alignments

Bioconductor version: 3.2

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: Herv\'e Pag\`es, Valerie Obenchain, Martin Morgan

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("GenomicAlignments")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicAlignments")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicAlignments")

PDF		Counting reads with summarizeOverlaps
PDF		Overlap encodings
PDF		Working with aligned nucleotides
PDF		Reference Manual
Text		NEWS
Video		Reading from a BAM file - Part 1
Video		Reading from a BAM file - Part 2

Details

biocViews	Alignment, Coverage, DataImport, Genetics, Infrastructure, RNASeq, SNP, Sequencing, Software
Version	1.6.3
In Bioconductor since	BioC 2.14 (R-3.1) (2 years)
License	Artistic-2.0
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.15.3), S4Vectors(>= 0.8.6), IRanges(>= 2.3.21), GenomeInfoDb(>= 1.1.20), GenomicRanges(>= 1.21.6), SummarizedExperiment(>= 0.3.1), Biostrings(>= 2.37.1), Rsamtools(>= 1.21.4)
Imports	methods, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel
LinkingTo	S4Vectors, IRanges
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, DESeq, edgeR, RUnit, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me	AllelicImbalance, Basic4Cseq, chimera, DiffBind, exomePeak, GoogleGenomics, groHMM, Guitar, hiReadsProcessor, prebs, RIPSeeker, rnaSeqMap, ShortRead, SplicingGraphs
Imports Me	biovizBase, ChIPQC, CNEr, CopywriteR, CoverageView, csaw, customProDB, derfinder, easyRNASeq, FourCSeq, genomation, GenomicFiles, ggbio, gmapR, GreyListChIP, Gviz, HTSeqGenie, INSPEcT, leeBamViews, metagene, methylPipe, PICS, QuasR, Repitools, RiboProfiling, RNAprobR, roar, Rqc, rtracklayer, SGSeq, similaRpeak, soGGi, SplicingGraphs, trackViewer
Suggests Me	BiocParallel, gage, GenomeInfoDb, GenomicFeatures, GenomicRanges, oneChannelGUI, parathyroidSE, RNAseqData.HNRNPC.bam.chr14, RnaSeqTutorial, Rsamtools, Streamer
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	GenomicAlignments_1.6.3.tar.gz
Windows Binary	GenomicAlignments_1.6.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GenomicAlignments_1.6.1.tgz
Mac OS X 10.9 (Mavericks)	GenomicAlignments_1.6.3.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/GenomicAlignments/tree/release-3.2
Package Short Url	http://bioconductor.org/packages/GenomicAlignments/
Package Downloads Report	Download Stats

Documentation »

Bioconductor

Package vignettes and manuals.
Workflows for learning and use.
Course and conference material.
Videos.
Community resources and tutorials.

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Support site - for questions about Bioconductor packages
Bioc-devel mailing list - for package developers