GenomicAlignments

DOI: 10.18129/B9.bioc.GenomicAlignments    

Representation and manipulation of short genomic alignments

Bioconductor version: Release (3.13)

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>

Installation

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

if (!requireNamespace("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	1.28.0
In Bioconductor since	BioC 2.14 (R-3.1) (7.5 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(>= 1.41.5), 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, rnaSeqMap, SCATEData, sequencing, ShortRead, SplicingGraphs
Imports Me	alpine, AneuFinder, APAlyzer, ASpediaFI, ASpli, ATACseqQC, 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, RNAprobR, roar, Rqc, rtracklayer, SCATE, scruff, seqplots, seqsetvis, SGSeq, soGGi, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, TAPseq, TarSeqQC, TCseq, trackViewer, transcriptR, TSRchitect, Ularcirc, UMI4Cats, VaSP, VplotR
Suggests Me	alpineData, amplican, 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_1.28.0.tar.gz
Windows Binary	GenomicAlignments_1.28.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	GenomicAlignments_1.28.0.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