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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 (3.19)

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 [aut, cre], Valerie Obenchain [aut], Martin Morgan [aut], Fedor Bezrukov [ctb], Robert Castelo [ctb]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An Introduction to the GenomicAlignments Package PDF R Script
Counting reads with summarizeOverlaps PDF R Script
Overlap encodings PDF R Script
Working with aligned nucleotides PDF R Script
Reference Manual PDF
Reading from a BAM file - Part 1 Video
Reading from a BAM file - Part 2 Video


biocViews Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software
Version 1.39.4
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), GenomeInfoDb(>= 1.13.1), GenomicRanges(>= 1.55.3), SummarizedExperiment(>= 1.9.13), Biostrings(>= 2.55.7), Rsamtools(>= 1.31.2)
Imports methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel
System Requirements
URL https://bioconductor.org/packages/GenomicAlignments
Bug Reports https://github.com/Bioconductor/GenomicAlignments/issues
See More
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, DESeq2, edgeR, RUnit, BiocStyle
Linking To S4Vectors, IRanges
Depends On Me AllelicImbalance, Basic4Cseq, BasicSTARRseq, ChIPexoQual, groHMM, HelloRanges, hiReadsProcessor, igvR, ORFik, prebs, recoup, RiboDiPA, sequencing, ShortRead, SplicingGraphs
Imports Me AneuFinder, APAlyzer, ASpli, ATACseqQC, ATACseqTFEA, atena, BaalChIP, bambu, biovizBase, breakpointR, BRGenomics, CAGEfightR, CAGEr, cfDNAPro, chimeraviz, ChIPpeakAnno, ChIPQC, chromstaR, CNEr, consensusDE, contiBAIT, CoverageView, CrispRVariants, CSSQ, customProDB, DAMEfinder, DegNorm, derfinder, DEScan2, DiffBind, DNAfusion, easyRNASeq, esATAC, exomePeak2, FLAMES, FRASER, FunChIP, gcapc, gDNAx, genomation, GenomicFiles, GenomicPlot, ggbio, gmapR, gmoviz, GreyListChIP, GUIDEseq, Gviz, HTSeqGenie, icetea, IMAS, INSPEcT, IntEREst, leeBamViews, MADSEQ, MDTS, metagene, metagene2, metaseqR2, methylPipe, mosaics, Motif2Site, msgbsR, NADfinder, PICS, plyranges, pram, proActiv, raer, ramwas, Repitools, RiboProfiling, ribosomeProfilingQC, RNAmodR, roar, Rqc, rtracklayer, saseR, scPipe, scruff, seqsetvis, SGSeq, single, soGGi, spiky, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, TAPseq, TCseq, trackViewer, transcriptR, Ularcirc, UMI4Cats, VaSP, VplotR, ZygosityPredictor
Suggests Me amplican, BindingSiteFinder, BiocParallel, csaw, DEXSeq, EpiCompare, ExperimentHub, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GenomicTuples, igvShiny, IRanges, NanoporeRNASeq, parathyroidSE, QuasR, RNAseqData.HNRNPC.bam.chr14, Rsamtools, SARC, similaRpeak, Streamer, systemPipeR
Links To Me
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Package Archives

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

Source Package GenomicAlignments_1.39.4.tar.gz
Windows Binary GenomicAlignments_1.39.4.zip (64-bit only)
macOS Binary (x86_64) GenomicAlignments_1.39.4.tgz
macOS Binary (arm64) GenomicAlignments_1.39.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicAlignments
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicAlignments
Bioc Package Browser https://code.bioconductor.org/browse/GenomicAlignments/
Package Short Url https://bioconductor.org/packages/GenomicAlignments/
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