Biostrings

DOI:10.18129 / B9.bioc.Biostrings

此包适用于Bioconductor 3.12版本;有关稳定的最新发布版本,请参见Biostrings

生物弦的有效操作

Bioconductor版本:3.12

内存高效的字符串容器,字符串匹配算法和其他实用程序,用于快速操作大型生物序列或序列集。

作者:H. Pagès, P. Aboyoun, R. Gentleman, S. DebRoy

维护人员:H. Pagès

引文(从R内,输入引用(“Biostrings”)):

安装

要安装此包,请启动R(版本“4.0”)并输入:

如果(!requireNamespace("BiocManager", quiet = TRUE)) install.packages("BiocManager") BiocManager::install("Biostrings")

对于R的旧版本,请参考相应的Bioconductor释放

文档

要查看系统中安装的此包版本的文档,请启动R并输入:

browseVignettes(“Biostrings”)

PDF R脚本 Biostrings 2中定义的基本类的简短介绍
PDF 生物strings快速概述
PDF R脚本 处理探针序列信息
PDF R脚本 多重比对
PDF R脚本 成对序列比对
PDF 参考手册
文本 新闻

细节

biocViews 对齐DataImportDataRepresentation遗传学基础设施SequenceMatching测序软件
版本 2.58.0
在Bioconductor BioC 1.6 (R-2.1)或更早(> 16年)
许可证 艺术- 2.0
取决于 R(>= 3.5.0),方法,BiocGenerics(> = 0.31.5),S4Vectors(> = 0.27.12),IRanges(> = 2.23.9),XVector(> = 0.29.2)
进口 方法,utils, grDevices,图形,统计,蜡笔
链接 S4VectorsIRangesXVector
建议 BSgenome(> = 1.13.14),BSgenome.Celegans.UCSC.ce2(> = 1.3.11),BSgenome.Dmelanogaster.UCSC.dm3(> = 1.3.11),BSgenome.Hsapiens.UCSC.hg18drosophila2probehgu95av2probehgu133aprobeGenomicFeatures(> = 1.3.14),hgu95av2cdfaffy(> = 1.41.3),affydata(> = 1.11.5),RUnit
SystemRequirements
增强了 Rmpi
URL //www.andersvercelli.com/packages/Biostrings
BugReports https://github.com/Bioconductor/Biostrings/issues
全靠我 altcdfenvsamplicanBasic4Cseq大脑BSgenomechimeravizChIPanalyserChIPsim切肉刀食典委CRISPRseek解读deepSNVFDb.FANTOM4.promoters.hg19GeneRegionScangeneregulationGenomicAlignments哥特harbChIPHelloRangeshiReadsProcessoriPACJASPAR2014烤肉串MethTargetedNGSmethVisualminfiModstringsMotifDbmsa肌肉NestLink益生元pd.agpd.aragene.1.0.stpd.aragene.1.1.stpd.ath1.121501pd.barley1pd.bovgene.1.0.stpd.bovgene.1.1.stpd.bovinepd.bsubtilispd.cangene.1.0.stpd.cangene.1.1.stpd.caninepd.canine.2pd.celeganspd.chickenpd.chigene.1.0.stpd.chigene.1.1.stpd.chogene.2.0.stpd.chogene.2.1.stpd.citruspd.clariom.d.humanpd.clariom.s.humanpd.clariom.s.human.htpd.clariom.s.mousepd.clariom.s.mouse.htpd.clariom.s.ratpd.clariom.s.rat.htpd.cottonpd.cyngene.1.0.stpd.cyngene.1.1.stpd.cyrgene.1.0.stpd.cyrgene.1.1.stpd.cytogenetics.arraypd.drogene.1.0.stpd.drogene.1.1.stpd.drosgenome1pd.drosophila.2pd.e.coli.2pd.ecolipd.ecoli.asv2pd.elegene.1.0.stpd.elegene.1.1.stpd.equgene.1.0.stpd.equgene.1.1.stpd.felgene.1.0.stpd.felgene.1.1.stpd.fingene.1.0.stpd.fingene.1.1.stpd.genomewidesnp.5pd.genomewidesnp.6pd.guigene.1.0.stpd.guigene.1.1.stpd.hc.g110pd.hg.focuspd.hg.u133.plus.2pd.hg.u133apd.hg.u133a.2pd.hg.u133a.tagpd.hg.u133bpd.hg.u219pd.hg.u95apd.hg.u95av2pd.hg.u95bpd.hg.u95cpd.hg.u95dpd.hg.u95epd.hg18.60mer.exprpd.ht.hg.u133.plus.pmpd.ht.hg.u133apd.ht.mg.430apd.hta.2.0pd.hu6800pd.huex.1.0.st.v2pd.hugene.1.0.st.v1pd.hugene.1.1.st.v1pd.hugene.2.0.stpd.hugene.2.1.stpd.maizepd.mapping250k.nsppd.mapping250k.stypd.mapping50k.hind240pd.mapping50k.xba240pd.margene.1.0.stpd.margene.1.1.stpd.medgene.1.0.stpd.medgene.1.1.stpd.medicagopd.mg.u74apd.mg.u74av2pd.mg.u74bpd.mg.u74bv2pd.mg.u74cpd.mg.u74cv2pd.mirna.1.0pd.mirna.2.0pd.mirna.3.0pd.mirna.4.0pd.moe430apd.moe430bpd.moex.1.0.st.v1pd.mogene.1.0.st.v1pd.mogene.1.1.st.v1pd.mogene.2.0.stpd.mogene.2.1.stpd.mouse430.2pd.mouse430a.2pd.mta.1.0pd.mu11ksubapd.mu11ksubbpd.nugo.hs1a520180pd.nugo.mm1a520177pd.ovigene.1.0.stpd.ovigene.1.1.stpd.pae.g1apd.plasmodium.anophelespd.poplarpd.porcinepd.porgene.1.0.stpd.porgene.1.1.stpd.rabgene.1.0.stpd.rabgene.1.1.stpd.rae230apd.rae230bpd.raex.1.0.st.v1pd.ragene.1.0.st.v1pd.ragene.1.1.st.v1pd.ragene.2.0.stpd.ragene.2.1.stpd.rat230.2pd.rcngene.1.0.stpd.rcngene.1.1.stpd.rg.u34apd.rg.u34bpd.rg.u34cpd.rhegene.1.0.stpd.rhegene.1.1.stpd.rhesuspd.ricepd.rjpgene.1.0.stpd.rjpgene.1.1.stpd.rn.u34pd.rta.1.0pd.rusgene.1.0.stpd.rusgene.1.1.stpd.s.aureuspd.soybeanpd.soygene.1.0.stpd.soygene.1.1.stpd.sugar.canepd.tomatopd.u133.x3ppd.vitis.viniferapd.wheatpd.x.laevis.2pd.x.tropicalispd.xenopus.laevispd.yeast.2pd.yg.s98pd.zebgene.1.0.stpd.zebgene.1.1.stpd.zebrafishperiodicDNAPGApqsfinderPWMEnrichqrqcQSutilsR453Plus1ToolboxR4RNAREDseqrGADEMRiboProfilingRoleswitchrRDPRsamtoolsRSVSimsangeranalyseRsangerseqR扫描。通用产品scsRSELEXseqbias测序ShortReadSICtoolsSimFFPEssvizStructstringssystemPipeRtopdownr三层
进口我 AffyCompatibleAllelicImbalance高山AneuFinderAnnotationHubDataappreci8RArrayExpressHTSAssessORFATACseqQCBBCAnalyzerBCRANKbcSeq击败BgeeCallBioSeqClassbiovizBasebrainflowprobes分歧点BSgenomebsseqBUMHMMBUSpaRseCellaRepertoriumChIPpeakAnnoChIPseqRChIPsimchromVARcircRNAprofilercnCNVfilteRcompEpiToolsconsensusDE警戒线CrispRVariantscustomProDBdada2dagLogoDAMEfinderdecompTumor2SigdiffHicDNAshapeRDominoEffecteasyRNASeqEDASeqensembldbensemblVEPEpiTxDbesATACeudysbiomeEuPathDBEventPointerexomePeak2FastqCleanerFDb.InfiniumMethylation.hg18FDb.InfiniumMethylation.hg19FindMyFriendsFourCSeqGA4GHclientgcapcgcrmagenbankrGeneRegionScanGeneStructureToolsGenoGAMgenomationGenomicAlignmentsGenomicFeaturesGenomicScoresgenphenGenVisRggbioGGtoolsgirafegmapRgmovizGUIDEseqGvizgwascath5vc的热图希尔达HiTCHTSeqGenieiceteaidprIMMAN感兴趣InterMineR电离ipdDbIsoformSwitchAnalyzeRKEGGRESTLogolasLowMACALymphoSeqMACPETMADSEQMatrixRider联合化疗MEDIPSMEDMEMesKitmetagenomeFeaturesmetaseqR2methimputemethVisualmethylPipeMicrobiotaProcessMMDiff2motifbreakRmotifcountermotifmatchrmotifStackMotIVMSnIDMSstatsPTMmulticrisprmusicatkMutationalPatternsngsReports诊断oligoClassesOmaDBopenPrimeRORFikOTUbasepackFinderpd.081229.hg18.promoter.medip.hx1pd.2006.07.18.hg18.refseq.promoterpd.2006.07.18.mm8.refseq.promoterpd.2006.10.31.rn34.refseq.promoterpd.atdschip.tilingpd.charm.hg18.examplepd.feinberg.hg18.me.hx1pd.feinberg.mm8.me.hx1pd.mirna.3.1pdInfoBuilderPhyloProfilePhyloProfileDataphyloseqpipeFramepodkat聚酯primirTSSproBAMrprocoilProteomicsAnnotationHubDataPureCNPvizqPLEXanalyzerqrqcqseaQuasRr3Cseqramwas美国广播公司Rcpi地区regutoolsREMPRepitoolsrfaRmrGADEMribosomeProfilingQCRNAmodRRNAprobRRNASeqRRqcrtracklayer衬衣scmeth范围scoreInvHapscRepertoire颈背SeqArrayseqcomboseqPatternseqplotsSGSeq签名者SigsPackSNPhoodsoGGiSomaticSignaturesSparseSignatures分裂sscuStructuralVariantAnnotationsynapterSynExtendSynMutTAPseqTarSeqQCTFBSTools石棉水泥板trenatRNAtRNAdbImporttRNAscanImportTVTBtximetaUlarcircUMI4CatsuniversalmotifVariantAnnotationVariantExperimentVariantFilteringVariantToolswavClusteRYAPSA
建议我 注释AnnotationForgeAnnotationHubbambu强盗BeadArrayUseCasesBiocGenericsBRGenomicsCINdexCSAReisaRexomeCopyGenomicFilesGenomicRangesgenosetGWASToolsmaftoolsmethrixmethylumi海市蜃楼nuCposRNAmodR。AlkAnilineSeqrpxrSWeePrTRMSNPlocs.Hsapiens.dbSNP.20101109SNPlocs.Hsapiens.dbSNP.20120608SNPlocs.Hsapiens.dbSNP141.GRCh38SNPlocs.Hsapiens.dbSNP142.GRCh37SNPlocs.Hsapiens.dbSNP144.GRCh37SNPlocs.Hsapiens.dbSNP144.GRCh38SNPlocs.Hsapiens.dbSNP149.GRCh38SNPlocs.Hsapiens.dbSNP150.GRCh38SNPlocs.Hsapiens.dbSNP151.GRCh38飞溅treeioXtraSNPlocs.Hsapiens.dbSNP144.GRCh37XtraSNPlocs.Hsapiens.dbSNP144.GRCh38XVector
链接到我 解读烤肉串MatrixRiderRsamtoolsShortRead三层VariantAnnotationVariantFiltering
构建报告

包档案

遵循2021年欧洲杯比分预测 在R会话中使用此包的说明。

源包 Biostrings_2.58.0.tar.gz
Windows二进制 Biostrings_2.58.0.zip(32位和64位)
macOS 10.13 (High Sierra) Biostrings_2.58.0.tgz
源库 git克隆https://git.bioconductor.org/packages/Biostrings
源存储库(开发人员访问) git克隆git@git.bioconductor.org:packages/Biostrings
包短Url //www.andersvercelli.com/packages/Biostrings/
软件包下载报告 下载数据

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