GenomicAlignments

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 gmail.com>

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

Installation

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

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	1.40.0
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
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, HelloRanges, ORFik, RiboDiPA, ShortRead, SplicingGraphs, groHMM, hiReadsProcessor, igvR, prebs, recoup, sequencing
Imports Me	APAlyzer, ASpli, ATACseqQC, ATACseqTFEA, AneuFinder, BaalChIP, CAGEfightR, CAGEr, CNEr, CSSQ, ChIPQC, ChIPpeakAnno, CoverageView, CrispRVariants, DAMEfinder, DEScan2, DNAfusion, DegNorm, DiffBind, FLAMES, FRASER, GUIDEseq, GenomicFiles, GenomicPlot, GreyListChIP, Gviz, HTSeqGenie, IMAS, INSPEcT, IntEREst, MADSEQ, MDTS, Motif2Site, NADfinder, PICS, RNAmodR, Repitools, RiboProfiling, Rqc, SGSeq, SPLINTER, TAPseq, TCseq, UMI4Cats, Ularcirc, VaSP, VplotR, ZygosityPredictor, atena, bambu, biovizBase, breakpointR, cfDNAPro, chimeraviz, chromstaR, consensusDE, customProDB, derfinder, easyRNASeq, esATAC, gDNAx, gcapc, genomation, ggbio, gmapR, gmoviz, icetea, metagene2, metaseqR2, methylPipe, mosaics, msgbsR, plyranges, pram, proActiv, raer, ramwas, ribosomeProfilingQC, roar, rtracklayer, saseR, scPipe, scruff, seqsetvis, soGGi, spiky, srnadiff, strandCheckR, trackViewer, transcriptR, leeBamViews, alakazam, iimi, MAAPER, PACVr, VALERIE
Suggests Me	BindingSiteFinder, BiocParallel, DEXSeq, ExperimentHub, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GenomicTuples, IRanges, QuasR, Rsamtools, SARC, Streamer, amplican, csaw, gage, igvShiny, similaRpeak, systemPipeR, NanoporeRNASeq, parathyroidSE, RNAseqData.HNRNPC.bam.chr14, seqmagick
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	GenomicAlignments_1.40.0.tar.gz
Windows Binary (x86_64)	GenomicAlignments_1.40.0.zip
macOS Binary (x86_64)	GenomicAlignments_1.40.0.tgz
macOS Binary (arm64)	GenomicAlignments_1.40.0.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