BiocStyle

DOI: 10.18129/B9.bioc.BiocStyle    

Standard styles for vignettes and other Bioconductor documents

Bioconductor version: Release (3.16)

Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

Author: Andrzej OleĊ› [aut] , Mike Smith [ctb] , Martin Morgan [ctb], Wolfgang Huber [ctb], Bioconductor Package [cre]

Maintainer: Bioconductor Package <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocStyle")

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("BiocStyle")

 

HTML R Script Authoring R Markdown vignettes
PDF R Script Bioconductor LaTeX Style 2.0
PDF   Reference Manual
Text   NEWS

Details

biocViews Software
Version 2.26.0
In Bioconductor since BioC 2.13 (R-3.0) (9 years)
License Artistic-2.0
Depends
Imports bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager
LinkingTo
Suggests BiocGenerics, RUnit, htmltools
SystemRequirements
Enhances
URL https://github.com/Bioconductor/BiocStyle
BugReports https://github.com/Bioconductor/BiocStyle/issues
Depends On Me curatedBreastData, cytofWorkflow, ExpressionAtlas, methylationArrayAnalysis, netresponse, org.Mxanthus.db, Pigengene, rnaseqGene, RnaSeqGeneEdgeRQL, RPA, sangeranalyseR
Imports Me abseqR, ASpli, bandle, BiocWorkflowTools, BPRMeth, BubbleTree, chimeraviz, COMPASS, deco, DiscoRhythm, FieldEffectCrc, geneXtendeR, GeoMxWorkflows, Melissa, meshr, MSnID, PathoStat, PhyloProfile, PhyloProfileData, rebook, regionReport, Rmmquant, Rqc, scMET, scTensor, scTGIF, simpleSingleCell, srnadiff
Suggests Me ACE, ADAMgui, ADImpute, AffiXcan, affycoretools, aggregateBioVar, AHEnsDbs, AHLRBaseDbs, AHMeSHDbs, AHPathbankDbs, AHPubMedDbs, AHWikipathwaysDbs, ALDEx2, alevinQC, AllelicImbalance, AlpsNMR, AMOUNTAIN, amplican, AneuFinder, animalcules, annotation, AnnotationDbi, AnnotationFilter, AnnotationForge, AnnotationHub, AnnotationHubData, annotationTools, annotatr, anota2seq, AnVIL, AnVILBilling, AnVILPublish, APAlyzer, APL, arrayQualityMetrics, arrays, artMS, ASGSCA, ASICS, ASICSdata, AssessORF, AssessORFData, ASSIGN, ATACseqQC, ATACseqTFEA, atena, atSNP, AUCell, awst, BaalChIP, bacon, bamsignals, BANDITS, banocc, barcodetrackR, basecallQC, BASiCS, basilisk, basilisk.utils, batchelor, bayNorm, baySeq, beachmat, beadarray, BeadDataPackR, BEARscc, BEclear, beer, benchdamic, benchmarkfdrData2019, BgeeDB, bigmelon, BindingSiteFinder, bioassayR, Biobase, biobtreeR, bioCancer, BiocBaseUtils, BiocCheck, BiocDockerManager, BiocFileCache, BiocIO, BiocMetaWorkflow, BiocNeighbors, BiocOncoTK, BioCor, BiocParallel, BiocPkgTools, BiocSet, BiocSingular, BiocSklearn, biocthis, biocViews, biodb, biodbChebi, biodbExpasy, biodbHmdb, biodbKegg, biodbLipidmaps, biodbMirbase, biodbNcbi, biodbNci, biodbUniprot, BioImageDbs, biomaRt, biomformat, BioMM, BioNERO, BioPlex, biosigner, biotmle, biscuiteer, BitSeq, blacksheepr, blima, blimaTestingData, BloodCancerMultiOmics2017, bluster, bnbc, BOBaFIT, bodymapRat, borealis, brainflowprobes, BrainSABER, branchpointer, breakpointR, breakpointRdata, brendaDb, BRGenomics, BridgeDbR, BrowserViz, bsseq, bugsigdbr, BUMHMM, BumpyMatrix, BUScorrect, BUSpaRse, BUSseq, CAFE, CAGEfightR, cageminer, CAGEr, CAGEWorkflow, canceR, CancerInSilico, cardelino, Cardinal, CardinalWorkflows, CARNIVAL, CATALYST, cbaf, CBEA, cBioPortalData, cbpManager, ccfindR, ccImpute, ccrepe, celda, CellaRepertorium, CellBarcode, cellbaseR, CellBench, celldex, CelliD, cellity, CellMapper, CellMapperData, CellMixS, cellTree, cellxgenedp, censcyt, Cepo, CexoR, cfDNAPro, ChemmineDrugs, ChemmineOB, ChemmineR, Chicago, ChIPComp, chipenrich, chipenrich.data, ChIPexoQual, ChIPexoQualExample, ChIPpeakAnno, ChIPQC, chipseqDB, chipseqDBData, ChromSCape, chromstaR, chromswitch, CIMICE, CircSeqAlignTk, CiteFuse, ClassifyR, cleanUpdTSeq, cleaver, clipper, cliProfiler, CLLmethylation, clusterExperiment, clusterSeq, ClusterSignificance, clustifyr, clustifyrdatahub, cmapR, CNEr, CNVMetrics, CNVRanger, COCOA, CoGAPS, cogeqc, Cogito, comapr, coMET, coMethDMR, compcodeR, CompoundDb, conclus, CONFESS, consensusOV, consensusSeekeR, consICA, CONSTANd, contiBAIT, conumee, CopyhelpeR, CopyNeutralIMA, CopyNumberPlots, CopywriteR, coRdon, CoRegNet, CoreGx, corral, coseq, COSMIC.67, cosmiq, COTAN, covRNA, cpvSNP, crisprBowtie, crisprBwa, crisprDesign, crisprScore, crisprScoreData, CRISPRseek, CrispRVariants, crisprVerse, crisprViz, csaw, csawUsersGuide, csdR, CSSQ, CTCF, CTDquerier, ctgGEM, ctsGE, CTSV, curatedBladderData, curatedCRCData, curatedMetagenomicData, curatedOvarianData, curatedTBData, curatedTCGAData, customCMPdb, cydar, CyTOFpower, CytoGLMM, cytoKernel, cytomapper, CytoTree, dada2, dagLogo, DAMEfinder, DaMiRseq, DAPAR, dasper, dcanr, dce, ddPCRclust, debCAM, decompTumor2Sig, decontam, deconvR, decoupleR, DEFormats, DEGreport, DelayedArray, DelayedMatrixStats, DelayedRandomArray, DelayedTensor, demuxmix, densvis, DEP, DepecheR, depmap, DEqMS, derfinder, derfinderData, derfinderHelper, derfinderPlot, DEScan2, DEWSeq, DExMA, DExMAdata, DEXSeq, DIAlignR, DiffBind, diffcyt, DifferentialRegulation, diffuStats, diffUTR, Dino, dir.expiry, discordant, dittoSeq, DmelSGI, DMRScan, dmrseq, DNABarcodeCompatibility, DNABarcodes, DNAfusion, doppelgangR, dorothea, Doscheda, doseR, drawProteins, DRIMSeq, DropletTestFiles, DropletUtils, drugTargetInteractions, DSS, dStruct, DuoClustering2018, dupRadar, easier, easierData, easyreporting, easyRNASeq, EBImage, EDASeq, EGSEA, EGSEA123, eiR, eisaR, ELMER, ELMER.data, EmpiricalBrownsMethod, emtdata, EnrichmentBrowser, ensembldb, EpiCompare, EpiDISH, epigraHMM, EpiMix, epimutacions, epimutacionsData, epistack, epistasisGA, EpiTxDb, EpiTxDb.Hs.hg38, EpiTxDb.Mm.mm10, EpiTxDb.Sc.sacCer3, epivizr, epivizrChart, epivizrData, epivizrServer, epivizrStandalone, erma, ERSSA, escape, EuPathDB, evaluomeR, EventPointer, EWCE, ewceData, excluderanges, ExperimentHub, ExperimentHubData, ExperimentSubset, ExploreModelMatrix, ExpressionNormalizationWorkflow, extraChIPs, FamAgg, famat, FastqCleaner, fastreeR, fCCAC, fCI, fcScan, FEAST, FELLA, FilterFFPE, FindIT2, FLAMES, flowAI, flowcatchR, flowGraph, flowMap, FlowSOM, flowSpecs, fmcsR, fobitools, FRASER, furrowSeg, GA4GHclient, GA4GHshiny, GARS, GBScleanR, gcapc, GDSArray, gemma.R, genbankr, GeneAccord, GeneExpressionSignature, genefilter, genefu, GeneNetworkBuilder, GeneOverlap, geneplast, geneplast.data, generegulation, GENESIS, GeneStructureTools, GeneTonic, GenomAutomorphism, GenomeInfoDb, GenomicAlignments, GenomicDataCommons, GenomicDistributions, GenomicDistributionsData, GenomicFeatures, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicRanges, GenomicScores, GenomicState, GenomicSuperSignature, GenomicTuples, GenVisR, GeuvadisTranscriptExpr, ggbio, ggmanh, ggmsa, GGPA, ggspavis, GladiaTOX, Glimma, glmGamPoi, glmSparseNet, gmoviz, GMRP, GOexpress, GOfuncR, GOpro, goSorensen, goSTAG, gpart, gpuMagic, GRaNIE, granulator, graper, graph, graphite, GreyListChIP, GRmetrics, groHMM, GSAR, GSE103322, GSE13015, GSE159526, GSE62944, GSEABase, GSEABenchmarkeR, GSEAmining, GSgalgoR, GSVA, GUIDEseq, Gviz, GWAS.BAYES, gwascat, gwasurvivr, GWENA, Harman, HarmanData, hca, HCAData, HD2013SGI, HDCytoData, healthyControlsPresenceChecker, HelloRanges, HelloRangesData, hermes, Herper, HGC, HiCBricks, HiCDOC, HiContacts, HiContactsData, HighlyReplicatedRNASeq, highthroughputassays, Hiiragi2013, HiLDA, hipathia, HIREewas, HiTC, HMP16SData, HMP2Data, HPAanalyze, hpAnnot, hpar, HPiP, HTSFilter, HubPub, HumanAffyData, HumanTranscriptomeCompendium, ideal, iGC, IgGeneUsage, igvR, IHW, IHWpaper, illuminaio, imageHTS, IMAS, imcdatasets, imcRtools, immunoClust, immunotation, infercnv, InPAS, INSPEcT, InTAD, InteractionSet, InterCellar, InterMineR, IONiseR, iPath, IRanges, ISAnalytics, iSEE, iSEEhex, iSEEhub, iSEEu, ISLET, isomiRs, IVAS, JASPAR2022, karyoploteR, kissDE, LACE, ldblock, lefser, liftOver, lineagespot, LinkHD, Linnorm, lipidr, lisaClust, loci2path, LOLA, LoomExperiment, LowMACA, lpsymphony, LRBaseDbi, LRcell, LRcellTypeMarkers, m6Aboost, Macarron, MACPET, MACSr, made4, maEndToEnd, MAGeCKFlute, magrene, MAI, mAPKL, marr, maser, MassSpecWavelet, MAST, MatrixQCvis, MatrixRider, matter, MBASED, MBECS, mbkmeans, MBttest, MCbiclust, mCSEA, mCSEAdata, MEAL, MEAT, MEB, MEDIPS, megadepth, MerfishData, messina, metabCombiner, metabinR, MetaboAnnotation, MetaboCoreUtils, metabolomicsWorkbenchR, MetaboSignal, metagene, metagene2, MetaGxOvarian, MetaGxPancreas, MetaPhOR, metapod, metavizr, methimpute, methInheritSim, MethPed, MethReg, MethylAid, MethylAidData, methylCC, methylclock, methylInheritance, MethylMix, MethylSeqData, methylSig, MetNet, mfa, mia, miaSim, miaViz, microbiome, MicrobiomeBenchmarkData, microbiomeDataSets, microbiomeMarker, MIGSA, miloR, mimager, minfi, minionSummaryData, miQC, MIRA, miRcomp, miRmine, miRSM, miRspongeR, mirTarRnaSeq, missMethyl, missRows, mistyR, mixOmics, MMAPPR2, MMAPPR2data, MMDiff2, MMUPHin, moanin, MobilityTransformR, MODA, Modstrings, MOFA2, mogsa, MOMA, monaLisa, MoonlightR, mosbi, MOSim, Motif2Site, motifbreakR, MotifDb, motifStack, MouseFM, MouseGastrulationData, MouseThymusAgeing, mpra, MQmetrics, MSA2dist, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsCoreUtils, MsExperiment, MsFeatures, msigdb, msImpute, MSMB, MSnbase, MSPrep, msPurity, msqc1, msqrob2, MSstats, MSstatsLiP, MSstatsLOBD, MSstatsSampleSize, MSstatsTMT, MuData, MultiAssayExperiment, MultiBaC, multicrispr, MultiDataSet, multiGSEA, multiHiCcompare, multiMiR, multiSight, mumosa, MungeSumstats, muscat, muscData, musicatk, MutationalPatterns, MWASTools, mygene, myvariant, mzR, NADfinder, NanoStringDiff, NanoStringQCPro, nanotubes, NBSplice, ncGTW, ncRNAtools, ndexr, Nebulosa, NestLink, NetActivity, NetActivityData, netbiov, netboxr, netDx, nethet, netOmics, NetPathMiner, netprioR, netSmooth, NeuCA, NewWave, ngsReports, nnSVG, nondetects, NormalyzerDE, normr, NPARC, npGSEA, nucleoSim, nucleR, ODER, oligo, omicade4, omicRexposome, omicsPrint, omicsViewer, Omixer, OmnipathR, OnassisJavaLibs, OncoScore, OncoSimulR, ontoProc, optimalFlow, optimalFlowData, OPWeight, ORFhunteR, ORFik, Organism.dplyr, orthogene, Oscope, OUTRIDER, OVESEG, PAA, packFinder, padma, PAIRADISE, pairkat, PanomiR, PANTHER.db, PanViz, parathyroidSE, pareg, parglms, parody, pasilla, PasillaTranscriptExpr, Path2PPI, paxtoolsr, pcaExplorer, PCAN, PCHiCdata, PDATK, PeacoQC, peakPantheR, PepsNMR, PepsNMRData, phantasus, PharmacoGx, phastCons35way.UCSC.mm39, phenomis, phenopath, philr, PhIPData, PhosR, phyloP35way.UCSC.mm39, phyloseq, Pi, piano, pipeComp, plethy, plotGrouper, plyranges, pmp, pogos, POMA, PoTRA, powerTCR, POWSC, ppcseq, pqsfinder, pram, preciseTAD, preciseTADhub, PrecisionTrialDrawer, PrInCE, profileplyr, profileScoreDist, progeny, projectR, pRoloc, pRolocGUI, PROPER, Prostar, proteasy, ProteoDisco, ProteoMM, PSEA, PSMatch, ptairData, ptairMS, PureCN, PWMEnrich, qcmetrics, QDNAseq, QFeatures, qmtools, qpgraph, qsea, qsmooth, QSutils, qsvaR, Qtlizer, quantiseqr, quantro, QuasR, R3CPET, RadioGx, RaggedExperiment, rain, ramwas, RandomWalkRestartMH, randRotation, RAREsim, rat2302frmavecs, rawrr, Rbowtie, Rbwa, Rcade, rcellminer, rcellminerData, rCGH, RcisTarget, Rcwl, RcwlPipelines, RCX, RCy3, RCyjs, rDGIdb, ReactomePA, recount, recount3, recountmethylation, recountWorkflow, recoup, RedeR, RedisParam, regioneR, regioneReloaded, regsplice, regutools, ReQON, ResidualMatrix, RESOLVE, restfulSE, rexposome, rfaRm, Rfastp, RforProteomics, rfPred, RGMQL, RGMQLlib, RgnTX, rgoslin, RGraph2js, RGSEA, rhdf5, rhdf5client, rhdf5filters, Rhdf5lib, Rhisat2, Rhtslib, RiboCrypt, RiboProfiling, riboSeqR, ribosomeProfilingQC, rifi, RIVER, RJMCMCNucleosomes, RLHub, RLSeq, RMassBank, rmspc, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.Data, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAseq123, rnaseqcomp, RnaSeqSampleSize, RnaSeqSampleSizeData, Rnits, ROCpAI, rols, ropls, rprimer, rpx, rqt, rrvgo, Rsamtools, rScudo, rsemmed, rSWeeP, RTCGAToolbox, RTN, RTNduals, RTNsurvival, Rtpca, rTRM, RUVSeq, RVS, rWikiPathways, S4Vectors, sampleClassifier, sampleClassifierData, sangerseqR, satuRn, ScaledMatrix, scanMiR, scanMiRApp, scanMiRData, scATAC.Explorer, scater, scBubbletree, scCB2, scClassify, sccomp, scDblFinder, scDD, scDDboost, scds, scFeatureFilter, scifer, SCLCBam, scMerge, SCnorm, scone, scoreInvHap, scp, scPCA, scpdata, scran, scReClassify, ScreenR, scRepertoire, scRNAseq, scruff, scTreeViz, scuttle, sechm, segmentSeq, selectKSigs, seqArchR, seqCAT, SeqGate, seqLogo, seqPattern, seqsetvis, SeqSQC, sequencing, SeqVarTools, sesame, SEtools, sevenC, SGSeq, SharedObject, shinyMethyl, ShortRead, SIAMCAT, SigCheck, SigFuge, signatureSearch, signifinder, SigsPack, SimBenchData, SIMD, SimFFPE, similaRpeak, SIMLR, simpleSeg, sincell, single, Single.mTEC.Transcriptomes, SingleCellExperiment, SingleCellMultiModal, singleCellTK, SingleR, singscore, SingscoreAMLMutations, sitePath, slalom, slingshot, SMAD, snapcount, snifter, SNPediaR, SNPhood, SNPhoodData, soGGi, sojourner, SOMNiBUS, sparrow, sparseDOSSA, sparseMatrixStats, sparsenetgls, SparseSignatures, spaSim, SpatialCPie, spatialDE, SpatialExperiment, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, specL, Spectra, SpectralTAD, SPIAT, spicyR, SpidermiR, splatter, SPLINTER, splots, SpotClean, SPOTlight, spqn, SPsimSeq, sRACIPE, srnadiff, sSNAPPY, stageR, STAN, StarBioTrek, STATegRa, Statial, statTarget, STdeconvolve, STexampleData, strandCheckR, struct, Structstrings, structToolbox, SubCellBarCode, SUITOR, SummarizedBenchmark, SummarizedExperiment, sva, svaRetro, swfdr, switchde, synapsis, synapter, synaptome.data, SynExtend, syntenet, systemPipeR, systemPipeRdata, systemPipeShiny, systemPipeTools, TabulaMurisData, TabulaMurisSenisData, TADCompare, tanggle, TAPseq, TargetDecoy, TargetSearch, tartare, TBSignatureProfiler, TCGAbiolinks, TCGAbiolinksGUI, TCGAbiolinksGUI.data, TCGAutils, TEKRABber, TENxBrainData, TENxBUSData, TENxIO, TENxPBMCData, TENxVisiumData, terraTCGAdata, TFARM, TFBSTools, TFHAZ, TFutils, tidybulk, tidySingleCellExperiment, tidySummarizedExperiment, tigre, TileDBArray, timecoursedata, timeOmics, TimerQuant, tissueTreg, TMExplorer, TMixClust, TOAST, tomoda, tomoseqr, topconfects, topdownr, ToxicoGx, TPP, tracktables, trackViewer, TrajectoryUtils, transcriptogramer, transcriptR, transomics2cytoscape, TraRe, traseR, Travel, TreeAndLeaf, treekoR, TreeSummarizedExperiment, TREG, Trendy, TRESS, tricycle, tripr, tRNA, tRNAdbImport, tRNAscanImport, TRONCO, TTMap, tuberculosis, TurboNorm, TVTB, twoddpcr, txcutr, UCell, UCSCRepeatMasker, Ularcirc, UMI4Cats, uncoverappLib, UniProt.ws, updateObject, variancePartition, VariantAnnotation, VariantFiltering, variants, VariantToolsData, VCFArray, VDJdive, VectraPolarisData, velociraptor, VERSO, vidger, ViSEAGO, vissE, Voyager, vsclust, vsn, wateRmelon, wavClusteR, WeberDivechaLCdata, weitrix, wpm, xcms, xcore, Xeva, XNAString, yamss, YAPSA, zebrafishRNASeq, zellkonverter, zenith, zinbwave
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Follow Installation instructions to use this package in your R session.

Source Package BiocStyle_2.26.0.tar.gz
Windows Binary BiocStyle_2.26.0.zip
macOS Binary (x86_64) BiocStyle_2.26.0.tgz
macOS Binary (arm64) BiocStyle_2.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocStyle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocStyle
Package Short Url https://bioconductor.org/packages/BiocStyle/
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