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This is the development version of GenomicAlignments; for the stable release version, see GenomicAlignments.

Representation and manipulation of short genomic alignments

Bioconductor version: Development (3.3)

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: Hervé Pagès, Valerie Obenchain, Martin Morgan

Maintainer: Bioconductor Package Maintainer <maintainer at>

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


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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


biocViews Alignment, Coverage, DataImport, Genetics, Infrastructure, RNASeq, SNP, Sequencing, Software
Version 1.7.3
In Bioconductor since BioC 2.14 (R-3.1) (1.5 years)
License Artistic-2.0
Depends R (>= 2.10), methods, BiocGenerics(>= 0.15.3), S4Vectors(>= 0.7.1), 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
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, 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  

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Package Source GenomicAlignments_1.7.3.tar.gz
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