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

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see GenomicAlignments.

Representation and manipulation of short genomic alignments

Bioconductor version: 3.1

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 R Script Counting reads with summarizeOverlaps
PDF R Script Overlap encodings
PDF R Script 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 1.4.2
In Bioconductor since BioC 2.14 (R-3.1) (2 years)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.5.14), IRanges(>= 2.1.26), GenomeInfoDb(>= 1.1.20), GenomicRanges(>= 1.19.23), Biostrings(>= 2.35.1), Rsamtools(>= 1.19.39)
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, chimera, DiffBind, GoogleGenomics, groHMM, 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, leeBamViews, metagene, methylPipe, PICS, QuasR, Repitools, roar, rtracklayer, SGSeq, similaRpeak, soGGi, SplicingGraphs, systemPipeR, trackViewer
Suggests Me BiocParallel, gage, GenomeInfoDb, 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_1.4.2.tar.gz
Windows Binary GenomicAlignments_1.4.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomicAlignments_1.4.2.tgz
Mac OS X 10.9 (Mavericks) GenomicAlignments_1.4.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GenomicAlignments/tree/release-3.1
Package Short Url http://bioconductor.org/packages/GenomicAlignments/
Package Downloads Report Download Stats

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