GenomicAlignments
Representation and manipulation of short genomic alignments
Bioconductor version: 3.23 · Package version: 1.48.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicAlignments")Details
| Maintainer | Hervé Pagès <hpages.on.github@gmail.com> |
| 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.) |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/GenomicAlignments |
| Bug Reports | https://github.com/Bioconductor/GenomicAlignments/issues |
| Downloads rank | 25563 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software |
Documentation
- An Introduction to the GenomicAlignments Package
- Counting reads with summarizeOverlaps
- Overlap encodings
- Working with aligned nucleotides (WORK-IN-PROGRESS!)
Download
Dependencies
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)
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
Reverse dependencies
Depends On Me (14): AllelicImbalance, Basic4Cseq, BasicSTARRseq, ChIPexoQual, groHMM, HelloRanges, igvR, ORFik, prebs, recoup, RiboDiPA, sequencing, ShortRead, SplicingGraphs
Imports Me (96): alakazam, APAlyzer, ASpli, ATACseqQC, ATACseqTFEA, atena, BaalChIP, bambu, 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, IMAS, INSPEcT, IntEREst, leeBamViews, MDTS, metagene2, metaseqR2, methylPipe, mosaics, Motif2Site, MotifPeeker, msgbsR, NADfinder, PACVr, PICB, plyranges, pram, proActiv, profileplyr, raer, ramwas, RiboProfiling, ribosomeProfilingQC, RNAmodR, roar, Rqc, rtracklayer, saseR, scPipe, scruff, seqsetvis, SGSeq, soGGi, spiky, SPLINTER, srnadiff, strandCheckR, TAPseq, TCseq, trackViewer, transcriptR, Ularcirc, UMI4Cats, VALERIE, VaSP, VplotR, ZygosityPredictor
Suggests Me (26): amplican, BindingSiteFinder, BiocParallel, cigarillo, csaw, DEXSeq, EpiCompare, ExperimentHub, extraChIPs, futurize, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GenomicTuples, igblastr, igvShiny, IRanges, NanoporeRNASeq, QuasR, RNAseqData.HNRNPC.bam.chr14, Rsamtools, seqmagick, similaRpeak, systemPipeR