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GenomicAlignments

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

All versions 3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

Representation and manipulation of short genomic alignments


Bioconductor version: Development (3.24)

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 gmail.com>

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

Hervé Pagès, Valerie Obenchain, Martin Morgan. GenomicAlignments: Representation and manipulation of short genomic alignments. doi:10.18129/B9.bioc.GenomicAlignments, R package version 1.49.2, https://bioconductor.org/packages/GenomicAlignments.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("GenomicAlignments")

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

Documentation

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

browseVignettes("GenomicAlignments")
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 ManualPDF
NEWSText
VideoVideo
VideoVideo
Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software
Version1.49.2
In Bioconductor sinceBioC 2.14 (R-3.1) (12.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.47.6), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1)
Imports utils, stats, BiocParallel, cigarillo (>= 0.99.2)
System Requirements
URLhttps://bioconductor.org/packages/GenomicAlignments
Bug Reportshttps://github.com/Bioconductor/GenomicAlignments/issues
See More
Suggests SummarizedExperiment, 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
Enhances
Depends On Me AllelicImbalance, Basic4Cseq, BasicSTARRseq, ChIPexoQual, groHMM, HelloRanges, igvR, ORFik, prebs, recoup, RiboDiPA, sequencing, ShortRead, SplicingGraphs
Imports Me alakazam, ASpli, ATACseqQC, ATACseqTFEA, atena, BaalChIP, bambu, BamScale, biovizBase, breakpointR, CAGEfightR, CAGEr, cfDNAPro, chimeraviz, ChIPpeakAnno, ChIPQC, CNEr, CoverageView, CrispRVariants, crupR, CSSQ, customProDB, DAMEfinder, DegNorm, derfinder, DEScan2, DiffBind, DMRcaller, DNAfusion, DOTSeq, DuplexDiscovereR, easyRNASeq, esATAC, EventPointer, FLAMES, FRASER, gcapc, gDNAx, genomation, GenomicFiles, GenomicPlot, ggbio, gmapR, gmoviz, GreyListChIP, GUIDEseq, Gviz, icetea, iimi, INSPEcT, IntEREst, leeBamViews, MDTS, metagene2, metaseqR2, methylPipe, mosaics, Motif2Site, MotifPeeker, msgbsR, NADfinder, PACVr, PICB, plyranges, pram, proActiv, profileplyr, raer, ramwas, ribosomeProfilingQC, RNAmodR, roar, Rqc, rtracklayer, saseR, scPipe, scruff, seqsetvis, SGSeq, spiky, SPLINTER, srnadiff, strandCheckR, TAPseq, TCseq, trackViewer, transcriptR, Ularcirc, UMI4Cats, VALERIE, VplotR, ZygosityPredictor
Suggests Me amplican, BindingSiteFinder, BiocParallel, cigarillo, DEXSeq, EpiCompare, ExperimentHub, extraChIPs, futurize, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GenomicTuples, igblastr, igvShiny, IRanges, NanoporeRNASeq, QuasR, RNAseqData.HNRNPC.bam.chr14, Rsamtools, S4Cartographer, seqmagick, similaRpeak, systemPipeR
Links To Me
Build Report Build Report, r-universe

Package Archives

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

Source Package GenomicAlignments_1.49.2.tar.gz
Windows Binary (x86_64) GenomicAlignments_1.49.2.zip
macOS Binary (big-sur-x86_64) GenomicAlignments_1.49.2.tgz
macOS Binary (sonoma-arm64) GenomicAlignments_1.49.2.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/GenomicAlignments
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/GenomicAlignments
Package Short Url https://bioconductor.org/packages/GenomicAlignments/
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