Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Author: H. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy
Maintainer: H. Pagès <hpages at fredhutch.org>
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| biocViews |
Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software |
| Version |
2.44.2 |
| In Bioconductor since |
BioC 1.6 (R-2.1) or earlier (> 12.5 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 2.8.0), methods, BiocGenerics(>= 0.15.6), S4Vectors(>= 0.13.13), IRanges(>= 2.9.18), XVector(>= 0.11.6) |
| Imports |
graphics, methods, stats, utils |
| LinkingTo |
S4Vectors, IRanges, XVector |
| Suggests |
BSgenome(>= 1.13.14), BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures(>= 1.3.14), hgu95av2cdf, affy(>= 1.41.3), affydata(>= 1.11.5), RUnit |
| SystemRequirements |
|
| Enhances |
Rmpi |
| URL |
|
| Depends On Me |
altcdfenvs, Basic4Cseq, BRAIN, BSgenome, chimeraviz, ChIPpeakAnno, ChIPsim, cleaver, CODEX, CRISPRseek, DECIPHER, deepSNV, FDb.FANTOM4.promoters.hg19, GeneRegionScan, GenomicAlignments, genphen, GOTHiC, harbChIP, HelloRanges, hiReadsProcessor, iPAC, JASPAR2014, kebabs, MethTargetedNGS, methVisual, minfi, MotifDb, motifRG, motifStack, msa, muscle, oligo, oneChannelGUI, pcaGoPromoter, pd.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.ath1.121501, pd.barley1, pd.bovgene.1.0.st, pd.bovgene.1.1.st, pd.bovine, pd.bsubtilis, pd.cangene.1.0.st, pd.cangene.1.1.st, pd.canine, pd.canine.2, pd.celegans, pd.chicken, pd.chigene.1.0.st, pd.chigene.1.1.st, pd.chogene.2.0.st, pd.chogene.2.1.st, pd.citrus, pd.clariom.d.human, pd.clariom.s.human, pd.clariom.s.human.ht, pd.clariom.s.mouse, pd.clariom.s.mouse.ht, pd.clariom.s.rat, pd.clariom.s.rat.ht, pd.cotton, pd.cyngene.1.0.st, pd.cyngene.1.1.st, pd.cyrgene.1.0.st, pd.cyrgene.1.1.st, pd.cytogenetics.array, pd.drogene.1.0.st, pd.drogene.1.1.st, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.elegene.1.0.st, pd.elegene.1.1.st, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.fingene.1.0.st, pd.fingene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.guigene.1.0.st, pd.guigene.1.1.st, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.hg18.60mer.expr, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hta.2.0, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.hugene.2.0.st, pd.hugene.2.1.st, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.margene.1.0.st, pd.margene.1.1.st, pd.medgene.1.0.st, pd.medgene.1.1.st, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.4.0, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177, pd.ovigene.1.0.st, pd.ovigene.1.1.st, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.porgene.1.0.st, pd.porgene.1.1.st, pd.rabgene.1.0.st, pd.rabgene.1.1.st, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.ragene.2.0.st, pd.ragene.2.1.st, pd.rat230.2, pd.rcngene.1.0.st, pd.rcngene.1.1.st, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhegene.1.0.st, pd.rhegene.1.1.st, pd.rhesus, pd.rice, pd.rjpgene.1.0.st, pd.rjpgene.1.1.st, pd.rn.u34, pd.rta.1.0, pd.rusgene.1.0.st, pd.rusgene.1.1.st, pd.s.aureus, pd.soybean, pd.soygene.1.0.st, pd.soygene.1.1.st, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebgene.1.0.st, pd.zebgene.1.1.st, pd.zebrafish, PGA, pqsfinder, PWMEnrich, qrqc, R453Plus1Toolbox, R4RNA, REDseq, rGADEM, RiboProfiling, Roleswitch, rRDP, Rsamtools, RSVSim, sangerseqR, SCAN.UPC, scsR, SELEX, seqbias, ShortRead, SICtools, spliceSites, ssviz, systemPipeR, triplex, waveTiling |
| Imports Me |
AffyCompatible, AllelicImbalance, alpine, AneuFinder, AnnotationHubData, ArrayExpressHTS, ATACseqQC, BBCAnalyzer, BCRANK, BEAT, BioMedR, BioSeqClass, biovizBase, branchpointer, BSgenome, BUMHMM, charm, ChIPseqR, ChIPsim, CNEr, cobindR, compEpiTools, CrispRVariants, customProDB, dada2, dagLogo, diffHic, DNAshapeR, easyRNASeq, EDASeq, ensembldb, ensemblVEP, eudysbiome, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FindMyFriends, FourCSeq, GA4GHclient, gcapc, gcrma, genbankr, GeneRegionScan, GenoGAM, genomation, GenomicAlignments, GenomicFeatures, GenVisR, ggbio, GGtools, girafe, gmapR, GoogleGenomics, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiTC, HTSeqGenie, IntEREst, IONiseR, KEGGREST, LowMACA, LymphoSeq, MADSEQ, maftools, MatrixRider, MEDIPS, MEDME, metagenomeFeatures, methVisual, methylPipe, microRNA, MMDiff2, motifbreakR, motifcounter, motifRG, MotIV, MutationalPatterns, oligoClasses, OTUbase, Pbase, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter, pd.atdschip.tiling, pd.charm.hg18.example, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.mirna.3.1, pdInfoBuilder, phyloseq, podkat, polyester, proBAMr, procoil, ProteomicsAnnotationHubData, PureCN, Pviz, qrqc, qsea, QuasR, r3Cseq, ramwas, RCAS, Rcpi, REDseq, REMP, Repitools, rGADEM, RNAprobR, Rqc, rSFFreader, rtracklayer, SeqArray, seqPattern, seqplots, SGSeq, signeR, SNPhood, soGGi, SomaticSignatures, SPLINTER, sscu, synapter, TarSeqQC, TFBSTools, TVTB, VariantAnnotation, VariantFiltering, VariantTools, wavClusteR |
| Suggests Me |
annotate, AnnotationForge, AnnotationHub, BeadArrayUseCases, CINdex, CSAR, exomeCopy, GenomicFiles, GenomicRanges, genoset, ggtree, methylumi, microRNA, MiRaGE, rpx, rTRM, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, treeio, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector |
| Build Report |
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