To install this package, start R and enter:

source("http://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: Release (3.0)

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:

source("http://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 1.2.1
In Bioconductor since BioC 2.14 (R-3.1)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.2.2), IRanges(>= 1.99.27), GenomeInfoDb(>= 1.1.20), GenomicRanges(>= 1.17.42), Biostrings(>= 2.33.14), Rsamtools(>= 1.17.28)
Imports methods, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel
Suggests 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
System Requirements
URL
Depends On Me AllelicImbalance, chimera, DiffBind, groHMM, hiReadsProcessor, metagene, prebs, RIPSeeker, rnaSeqMap, ShortRead, SplicingGraphs
Imports Me biovizBase, ChIPQC, CNEr, CoverageView, csaw, customProDB, derfinder, easyRNASeq, exonfindR, FourCSeq, GenomicFiles, ggbio, gmapR, Gviz, HTSeqGenie, leeBamViews, methylPipe, PICS, QuasR, Repitools, roar, rtracklayer, SGSeq, SplicingGraphs, trackViewer
Suggests Me BiocParallel, gage, GenomeInfoDb, GenomicRanges, parathyroidSE, RNAseqData.HNRNPC.bam.chr14, RnaSeqTutorial, Rsamtools, Streamer

Package Archives

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

Package Source GenomicAlignments_1.2.1.tar.gz
Windows Binary GenomicAlignments_1.2.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomicAlignments_1.2.1.tgz
Mac OS X 10.9 (Mavericks) GenomicAlignments_1.2.1.tgz
Browse/checkout source (username/password: readonly)
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