GenomicAlignments

This is thedevelopment version of GenomicAlignments; for the stable release version, seeGenomicAlignments.

Representation and manipulation of short genomic alignments

DOI: 10.18129/B9.bioc.GenomicAlignments

Bioconductor version: Development (3.23)

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, entercitation("GenomicAlignments")):

Installation

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

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("GenomicAlignments")

For older versions of R, please refer to the appropriateBioconductor 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 Manual	PDF
NEWS	Text
	Video
	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment,Coverage,DataImport,Genetics,ImmunoOncology,Infrastructure,RNASeq,SNP,Sequencing,Software
Version	1.47.0
In Bioconductor since	BioC 2.14 (R-3.1) (11.5 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),SummarizedExperiment(>= 1.39.1),Biostrings(>= 2.77.2),Rsamtools(>= 2.25.1)
Imports	methods, utils, stats,BiocGenerics,S4Vectors,IRanges,GenomicRanges,Biostrings,Rsamtools,BiocParallel,cigarillo(>= 0.99.2)
System Requirements
URL	https://bioconductor.org/packages/GenomicAlignments
Bug Reports	https://github.com/Bioconductor/GenomicAlignments/issues

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
Enhances
Depends On Me	AllelicImbalance,Basic4Cseq,ChIPexoQual,groHMM,HelloRanges,igvR,ORFik,prebs,recoup,RiboDiPA,ShortRead,SplicingGraphs,sequencing
Imports Me	ASpli,ATACseqQC,ATACseqTFEA,atena,BaalChIP,bambu,biovizBase,breakpointR,CAGEfightR,CAGEr,cfDNAPro,chimeraviz,ChIPpeakAnno,CNEr,CoverageView,CrispRVariants,crupR,CSSQ,DAMEfinder,DegNorm,derfinder,DEScan2,DMRcaller,DNAfusion,DuplexDiscovereR,easyRNASeq,FLAMES,gcapc,gDNAx,genomation,GenomicFiles,GenomicPlot,ggbio,gmoviz,GreyListChIP,GUIDEseq,Gviz,icetea,INSPEcT,MDTS,metagene2,metaseqR2,methylPipe,mosaics,Motif2Site,MotifPeeker,msgbsR,NADfinder,PICB,plyranges,pram,proActiv,raer,ramwas,ribosomeProfilingQC,RNAmodR,roar,Rqc,rtracklayer,saseR,scPipe,scruff,seqsetvis,SGSeq,spiky,SPLINTER,srnadiff,strandCheckR,TAPseq,TCseq,trackViewer,UMI4Cats,VaSP,VplotR,ZygosityPredictor,leeBamViews,alakazam,iimi,MAAPER,PACVr,VALERIE
Suggests Me	amplican,BindingSiteFinder,BiocParallel,cigarillo,csaw,DEXSeq,EpiCompare,ExperimentHub,extraChIPs,gage,GenomeInfoDb,GenomicDataCommons,GenomicFeatures,GenomicRanges,GenomicTuples,igblastr,igvShiny,IRanges,QuasR,Rsamtools,similaRpeak,systemPipeR,NanoporeRNASeq,RNAseqData.HNRNPC.bam.chr14,seqmagick
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	GenomicAlignments_1.47.0.tar.gz
Windows Binary (x86_64)	GenomicAlignments_1.47.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)	GenomicAlignments_1.47.0.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/
Package Downloads Report	Download Stats

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