Representation and manipulation of short genomic alignments

Bioconductor version: Development (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>

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PDF R Script Counting reads with summarizeOverlaps
PDF R Script Overlap encodings
PDF R Script Working with aligned nucleotides
PDF   Reference Manual
Text   NEWS


biocViews DataImport, Genetics, Infrastructure, RNASeq, SNP, Sequencing, Software
Version 1.1.4
In Bioconductor since BioC 2.14 (R-3.1)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.7.7), S4Vectors(>= 0.0.1), IRanges(>= 1.99.1), GenomicRanges(>= 1.17.7), Biostrings(>= 2.33.3), Rsamtools(>= 1.17.5), BSgenome(>= 1.31.12)
Imports methods, stats, BiocGenerics, S4Vectors, 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
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, GenomicRanges, parathyroidSE, RNAseqData.HNRNPC.bam.chr14, RnaSeqTutorial, Rsamtools, Streamer

Package Downloads

Package Source GenomicAlignments_1.1.4.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomicAlignments_1.1.4.tgz
Mac OS X 10.9 (Mavericks)
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