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: 2.14

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

Details

biocViews	DataImport, Genetics, Infrastructure, RNASeq, SNP, Sequencing, Software
Version	1.0.6
In Bioconductor since	BioC 2.14 (R-3.1)
License	Artistic-2.0
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.7.7), IRanges(>= 1.21.25), GenomicRanges(>= 1.15.32), Biostrings(>= 2.31.10), Rsamtools(>= 1.15.26), BSgenome(>= 1.31.12)
Imports	methods, stats, BiocGenerics, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel
Suggests	rtracklayer, 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, prebs, RIPSeeker, rnaSeqMap, ShortRead, SplicingGraphs
Imports Me	biovizBase, ChIPQC, CNEr, CoverageView, customProDB, easyRNASeq, GenomicFiles, ggbio, gmapR, Gviz, HTSeqGenie, leeBamViews, PICS, QuasR, Repitools, roar, rtracklayer, SplicingGraphs, trackViewer
Suggests Me	DESeq2, gage, 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_1.0.6.tar.gz
Windows Binary	GenomicAlignments_1.0.6.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GenomicAlignments_1.0.6.tgz
Mac OS X 10.9 (Mavericks)	GenomicAlignments_1.0.6.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Oligonucleotide Arrays
High-throughput Sequencing
Counting Reads for Differential Expression (parathyroideSE vignette)
Annotation
Annotating Variants
Annotating Ranges
Flow Cytometry and other assays
Candidate Binding Sites for Known Transcription Factors
Cloud-enabled cis-eQTL search and annotation

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