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Representation and manipulation of short genomic alignments

Bioconductor version: Release (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], Halimat C. Atanda [ctb] (Translated 'WorkingWithAlignedNucleotides' vignette from Sweave to RMarkdown / HTML.)

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

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


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

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


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 (WORK-IN-PROGRESS!) HTML 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 1.40.0
In Bioconductor since BioC 2.14 (R-3.1) (10.5 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
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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, knitr, BiocStyle
Linking To S4Vectors, IRanges
Depends On Me AllelicImbalance, Basic4Cseq, ChIPexoQual, groHMM, HelloRanges, hiReadsProcessor, igvR, ORFik, prebs, recoup, RiboDiPA, ShortRead, SplicingGraphs, sequencing
Imports Me AneuFinder, APAlyzer, ASpli, ATACseqQC, ATACseqTFEA, atena, BaalChIP, bambu, biovizBase, breakpointR, CAGEfightR, CAGEr, cfDNAPro, chimeraviz, ChIPpeakAnno, ChIPQC, chromstaR, CNEr, consensusDE, CoverageView, CrispRVariants, CSSQ, customProDB, DAMEfinder, DegNorm, derfinder, DEScan2, DiffBind, DNAfusion, easyRNASeq, esATAC, FLAMES, FRASER, gcapc, gDNAx, genomation, GenomicFiles, GenomicPlot, ggbio, gmapR, gmoviz, GreyListChIP, GUIDEseq, Gviz, HTSeqGenie, icetea, IMAS, INSPEcT, IntEREst, MADSEQ, MDTS, 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, soGGi, spiky, SPLINTER, srnadiff, strandCheckR, TAPseq, TCseq, trackViewer, transcriptR, Ularcirc, UMI4Cats, VaSP, VplotR, ZygosityPredictor, leeBamViews, alakazam, iimi, MAAPER, PACVr, VALERIE
Suggests Me amplican, BindingSiteFinder, BiocParallel, csaw, DEXSeq, ExperimentHub, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GenomicTuples, igvShiny, IRanges, QuasR, Rsamtools, SARC, similaRpeak, Streamer, systemPipeR, NanoporeRNASeq, parathyroidSE, RNAseqData.HNRNPC.bam.chr14, seqmagick
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Source Package GenomicAlignments_1.40.0.tar.gz
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macOS Binary (arm64) GenomicAlignments_1.40.0.tgz
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