GenomicAlignments

DOI: 10.18129/B9.bioc.GenomicAlignments    

Representation and manipulation of short genomic alignments

Bioconductor version: Release (3.14)

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 bioconductor.org>

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

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

PDF R Script 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   Reference Manual
Text   NEWS
Video   Reading from a BAM file - Part 1
Video   Reading from a BAM file - Part 2

Details

biocViews Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software
Version 1.30.0
In Bioconductor since BioC 2.14 (R-3.1) (8 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(>= 1.41.5), SummarizedExperiment(>= 1.9.13), Biostrings(>= 2.55.7), Rsamtools(>= 1.31.2)
Imports methods, utils, 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, DESeq2, edgeR, RUnit, BiocStyle
SystemRequirements
Enhances
URL https://bioconductor.org/packages/GenomicAlignments
BugReports https://github.com/Bioconductor/GenomicAlignments/issues
Depends On Me AllelicImbalance, alpineData, Basic4Cseq, BasicSTARRseq, ChIPexoQual, groHMM, HelloRanges, hiReadsProcessor, igvR, ORFik, prebs, recoup, RiboDiPA, SCATEData, sequencing, ShortRead, SplicingGraphs
Imports Me alpine, AneuFinder, APAlyzer, ASpediaFI, ASpli, ATACseqQC, atena, BaalChIP, bambu, biovizBase, breakpointR, BRGenomics, CAGEfightR, CAGEr, chimeraviz, ChIPpeakAnno, ChIPQC, chromstaR, CNEr, consensusDE, contiBAIT, CopywriteR, CoverageView, CrispRVariants, CSSQ, customProDB, DAMEfinder, DegNorm, derfinder, DEScan2, DiffBind, easyRNASeq, exomePeak2, FRASER, FunChIP, gcapc, GenoGAM, genomation, GenomicFiles, ggbio, gmapR, gmoviz, GreyListChIP, GUIDEseq, Gviz, HTSeqGenie, icetea, IMAS, INSPEcT, IntEREst, leeBamViews, MACPET, MADSEQ, MDTS, metagene, metagene2, metaseqR2, methylPipe, mosaics, msgbsR, NADfinder, PICS, plyranges, pram, proActiv, ramwas, Rcade, Repitools, RiboProfiling, ribosomeProfilingQC, RNAmodR, roar, Rqc, rtracklayer, SCATE, scruff, seqsetvis, SGSeq, soGGi, spiky, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, TAPseq, TarSeqQC, TCseq, trackViewer, transcriptR, TSRchitect, Ularcirc, UMI4Cats, VaSP, VplotR
Suggests Me alpineData, amplican, BindingSiteFinder, BiocParallel, csaw, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, IRanges, NanoporeRNASeq, parathyroidSE, QuasR, RNAseqData.HNRNPC.bam.chr14, Rsamtools, similaRpeak, Streamer, systemPipeR
Links To Me
Build Report  

Package Archives

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

Source Package GenomicAlignments_1.30.0.tar.gz
Windows Binary GenomicAlignments_1.30.0.zip
macOS 10.13 (High Sierra) GenomicAlignments_1.30.0.tgz
Source Repository git 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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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