BiocStyle

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see BiocStyle.

Standard styles for vignettes and other Bioconductor documents


Bioconductor version: 3.13

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

Author: Andrzej OleÅ› [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 "4.1") 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")
Authoring R Markdown vignettes HTML R Script
Bioconductor LaTeX Style 2.0 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Software
Version 2.20.2
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License Artistic-2.0
Depends
Imports bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager
System Requirements
URL https://github.com/Bioconductor/BiocStyle
Bug Reports https://github.com/Bioconductor/BiocStyle/issues
See More
Suggests BiocGenerics, RUnit, htmltools
Linking To
Enhances
Depends On Me curatedBreastData, cytofWorkflow, methylationArrayAnalysis, org.Mxanthus.db, Pigengene, rnaseqGene, RnaSeqGeneEdgeRQL, sangeranalyseR
Imports Me abseqR, ASpli, BiocWorkflowTools, BPRMeth, BubbleTree, chimeraviz, COMPASS, deco, DiscoRhythm, FieldEffectCrc, geneXtendeR, Melissa, MSnID, PathoStat, PhyloProfile, PhyloProfileData, rebook, regionReport, Rmmquant, Rqc, scTensor, scTGIF, simpleSingleCell, srnadiff
Suggests Me ABAData, ABAEnrichment, ACE, ADAMgui, ADImpute, AffiXcan, affycoretools, aggregateBioVar, AHEnsDbs, AHLRBaseDbs, AHMeSHDbs, AHPathbankDbs, AHPubMedDbs, AHWikipathwaysDbs, ALDEx2, alevinQC, AllelicImbalance, AMOUNTAIN, amplican, AneuFinder, animalcules, annotation, AnnotationDbi, AnnotationFilter, AnnotationForge, AnnotationHub, AnnotationHubData, annotationTools, annotatr, anota2seq, AnVILBilling, AnVILPublish, APAlyzer, arrayQualityMetrics, arrays, artMS, ASGSCA, ASICS, ASICSdata, AssessORF, AssessORFData, ASSIGN, ATACseqQC, atSNP, AUCell, awst, BaalChIP, bacon, bamsignals, BANDITS, barcodetrackR, basecallQC, BASiCS, basilisk, basilisk.utils, batchelor, bayNorm, baySeq, beachmat, beadarray, BeadDataPackR, BEARscc, BEclear, benchmarkfdrData2019, BgeeDB, bigmelon, bigmemoryExtras, bioassayR, biobtreeR, bioCancer, BiocCheck, BiocDockerManager, BiocFileCache, BiocIO, BiocMetaWorkflow, BiocNeighbors, BiocOncoTK, BioCor, BiocParallel, BiocPkgTools, BiocSet, BiocSingular, BiocSklearn, biocthis, biodb, BioImageDbs, biomaRt, biomformat, BioMM, BioNERO, biosigner, biotmle, BitSeq, blacksheepr, blima, blimaTestingData, BloodCancerMultiOmics2017, bluster, bnbc, bodymapRat, brainflowprobes, BrainSABER, branchpointer, breakpointR, breakpointRdata, brendaDb, BRGenomics, BridgeDbR, BrowserViz, bsseq, BUMHMM, BumpyMatrix, BUScorrect, BUSpaRse, CAFE, CAGEfightR, CAGEr, CAGEWorkflow, CancerInSilico, CAnD, Cardinal, CardinalWorkflows, CATALYST, cbaf, cBioPortalData, cbpManager, ccfindR, ccrepe, celda, CellaRepertorium, cellbaseR, CellBench, celldex, CelliD, cellity, CellMapper, CellMapperData, CellMixS, cellTree, censcyt, CexoR, ChemmineDrugs, ChemmineOB, ChemmineR, Chicago, ChIPComp, chipenrich, chipenrich.data, ChIPexoQual, ChIPexoQualExample, ChIPpeakAnno, ChIPQC, chipseqDB, chipseqDBData, ChIPSeqSpike, ChromSCape, chromstaR, chromswitch, CIMICE, CiteFuse, ClassifyR, cleanUpdTSeq, cleaver, clipper, CLLmethylation, clusterExperiment, clusterSeq, ClusterSignificance, clustifyr, clustifyrdatahub, cmapR, CNEr, CNVRanger, COCOA, CoGAPS, coMET, compcodeR, conclus, CONFESS, consensusOV, consensusSeekeR, CONSTANd, contiBAIT, conumee, CopyhelpeR, CopyNeutralIMA, CopyNumberPlots, CopywriteR, coRdon, CoRegNet, CoreGx, corral, coseq, COSMIC.67, cosmiq, CountClust, covRNA, cpvSNP, CRISPRseek, CrispRVariants, csaw, csawUsersGuide, CSSQ, CTDquerier, ctgGEM, ctsGE, curatedBladderData, curatedCRCData, curatedMetagenomicData, curatedOvarianData, curatedTCGAData, customCMPdb, cydar, cytofast, CytoGLMM, cytomapper, CytoTree, dada2, dagLogo, DAMEfinder, DaMiRseq, DAPAR, dasper, dcanr, dce, ddPCRclust, debCAM, decompTumor2Sig, decontam, decoupleR, DEFormats, DEGreport, DelayedArray, DelayedMatrixStats, DelayedRandomArray, densvis, DEP, DepecheR, depmap, DEqMS, derfinder, derfinderData, derfinderHelper, derfinderPlot, DEScan2, DEWSeq, DExMA, DExMAdata, DEXSeq, DIAlignR, DiffBind, diffcyt, diffuStats, diffUTR, dir.expiry, discordant, dittoSeq, DmelSGI, DMRScan, dmrseq, DNABarcodeCompatibility, DNABarcodes, doppelgangR, dorothea, Doscheda, doseR, drawProteins, DRIMSeq, DropletTestFiles, DropletUtils, drugTargetInteractions, DSS, DuoClustering2018, dupRadar, easyreporting, easyRNASeq, EBImage, EDASeq, EGSEA, EGSEA123, eiR, eisaR, ELMER, ELMER.data, EmpiricalBrownsMethod, emtdata, EnrichmentBrowser, ensembldb, EpiDISH, epigraHMM, EpiTxDb, EpiTxDb.Hs.hg38, EpiTxDb.Mm.mm10, EpiTxDb.Sc.sacCer3, epivizr, epivizrChart, epivizrData, epivizrServer, epivizrStandalone, eQTL, erma, ERSSA, escape, EuPathDB, evaluomeR, EventPointer, EWCE, ewceData, ExperimentHub, ExperimentHubData, ExperimentSubset, ExploreModelMatrix, ExpressionNormalizationWorkflow, FamAgg, famat, FastqCleaner, fCCAC, fCI, fcScan, FEAST, FELLA, FilterFFPE, FindMyFriends, flowAI, flowcatchR, flowGraph, flowMap, FlowSOM, flowSpecs, fmcsR, fobitools, FRASER, furrowSeg, GA4GHclient, GA4GHshiny, GARS, gcapc, GCSConnection, GCSFilesystem, GDSArray, genbankr, GeneAccord, GeneExpressionSignature, genefilter, genefu, GeneNetworkBuilder, GeneOverlap, geneplast, generegulation, GENESIS, GeneStructureTools, GeneTonic, GenoGAM, GenomeInfoDb, GenomicAlignments, GenomicDataCommons, GenomicDistributions, GenomicDistributionsData, GenomicFeatures, GenomicFiles, GenomicInteractions, GenomicRanges, GenomicScores, GenomicState, GenomicSuperSignature, GenomicTuples, genoset, GenVisR, GeuvadisTranscriptExpr, ggbio, GGPA, GladiaTOX, Glimma, glmGamPoi, glmSparseNet, gmoviz, GMRP, GOexpress, GOfuncR, GOpro, goSTAG, gpart, gpuMagic, granulator, graper, graphite, GreyListChIP, GRmetrics, groHMM, GSAR, GSE13015, GSE62944, GSEABase, GSEABenchmarkeR, GSEAmining, GSgalgoR, GSVA, GUIDEseq, Gviz, GWAS.BAYES, gwascat, gwasurvivr, GWENA, Harman, HarmanData, hca, HCABrowser, HCAData, HCAExplorer, HCAMatrixBrowser, HD2013SGI, HDCytoData, HelloRanges, HelloRangesData, Herper, HGC, HiCBricks, HighlyReplicatedRNASeq, highthroughputassays, Hiiragi2013, HiLDA, hipathia, HIREewas, HiTC, HMP16SData, HMP2Data, HPAanalyze, hpAnnot, hpar, HTSFilter, HubPub, HumanAffyData, HumanTranscriptomeCompendium, ideal, iGC, IgGeneUsage, igvR, IHW, IHWpaper, illuminaio, imageHTS, IMAS, imcdatasets, Imetagene, immunoClust, immunotation, infercnv, InPAS, INSPEcT, InTAD, InteractionSet, InterCellar, InterMineR, IONiseR, IRanges, ISAnalytics, iSEE, iSEEu, isomiRs, IVAS, JctSeqData, karyoploteR, kissDE, LACE, ldblock, lefser, liftOver, LinkHD, Linnorm, lipidr, lisaClust, loci2path, LOLA, LoomExperiment, LowMACA, lpsymphony, LRBaseDbi, LRcell, LRcellTypeMarkers, MACPET, MACSr, made4, maEndToEnd, MAGeCKFlute, mAPKL, marr, maser, MAST, MatrixQCvis, MatrixRider, matter, MBASED, mbkmeans, MBttest, MCbiclust, mCSEA, mCSEAdata, mdgsa, MEAL, MEAT, MEB, MEDIPS, megadepth, messina, metabCombiner, MetaboCoreUtils, metabolomicsWorkbenchR, MetaboSignal, metagene, metagene2, metagenomeFeatures, MetaGxPancreas, metapod, metavizr, methimpute, methInheritSim, MethPed, MethReg, MethylAid, MethylAidData, methylCC, methylInheritance, MethylMix, MethylSeqData, methylSig, MetNet, mfa, mia, miaViz, microbiome, microbiomeDataSets, MIGSA, miloR, mimager, minfi, minionSummaryData, miQC, MIRA, miRcomp, miRmine, miRSM, miRspongeR, mirTarRnaSeq, missMethyl, missRows, mistyR, mixOmics, MLSeq, MMAPPR2, MMAPPR2data, MMDiff2, MMUPHin, moanin, MODA, Modstrings, MOFA2, MOGAMUN, mogsa, MOMA, MoonlightR, MOSim, motifbreakR, MotifDb, motifStack, MouseFM, MouseGastrulationData, MouseThymusAgeing, mpra, MsBackendMassbank, MsBackendMgf, MsCoreUtils, MSEADbi, MsFeatures, msigdb, msImpute, MSMB, MSnbase, MSPrep, msPurity, msqc1, msqrob2, MSstats, MSstatsBioData, MSstatsLOBD, MSstatsPTM, MSstatsSampleSize, MSstatsTMT, MSstatsTMTPTM, 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, netbiov, netboxr, netDx, nethet, NetPathMiner, netprioR, netSmooth, NewWave, ngsReports, nondetects, NormalyzerDE, normr, NPARC, npGSEA, nucleoSim, nucleR, oligo, omicade4, omicRexposome, omicsPrint, Omixer, OmnipathR, Onassis, OnassisJavaLibs, OncoScore, OncoSimulR, ontoProc, optimalFlow, optimalFlowData, OPWeight, ORFhunteR, ORFik, Organism.dplyr, Oscope, OUTRIDER, OVESEG, PAA, packFinder, padma, PAIRADISE, PANTHER.db, PanVizGenerator, parathyroidSE, parglms, parody, pasilla, PasillaTranscriptExpr, Path2PPI, paxtoolsr, pcaExplorer, PCAN, PCHiCdata, PDATK, PeacoQC, peakPantheR, PepsNMR, PepsNMRData, perturbatr, phantasus, phenopath, philr, PhIPData, PhosR, phyloseq, Pi, piano, pipeComp, plethy, plotGrouper, plyranges, pmp, Polyfit, POMA, PoTRA, powerTCR, POWSC, ppcseq, pqsfinder, pram, preciseTAD, preciseTADhub, PrecisionTrialDrawer, PrInCE, profileplyr, profileScoreDist, progeny, projectR, pRoloc, pRolocGUI, PROPER, Prostar, proteomics, ProteomicsAnnotationHubData, ProteoMM, PSEA, ptairData, ptairMS, PureCN, PWMEnrich, qcmetrics, QDNAseq, QFeatures, qpgraph, qsea, qsmooth, QSutils, Qtlizer, quantiseqr, quantro, QuasR, R3CPET, RadioGx, RaggedExperiment, rain, ramwas, RandomWalkRestartMH, randRotation, rat2302frmavecs, rawrr, Rbowtie, Rcade, rcellminer, rcellminerData, rCGH, RcisTarget, Rcwl, RcwlPipelines, RCy3, RCyjs, rDGIdb, ReactomePA, recount, recount3, recountmethylation, recountWorkflow, recoup, RedeR, regioneR, regsplice, regutools, ReQON, ResidualMatrix, restfulSE, rexposome, rfaRm, Rfastp, RforProteomics, rfPred, RGMQL, RGMQLlib, RGraph2js, RGSEA, rhdf5, rhdf5client, rhdf5filters, Rhdf5lib, Rhisat2, Rhtslib, RiboProfiling, riboSeqR, ribosomeProfilingQC, RIVER, RJMCMCNucleosomes, RMassBank, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.Data, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAprobR, RNAseq123, rnaseqcomp, RnaSeqSampleSize, RnaSeqSampleSizeData, Rnits, ROCpAI, rols, ropls, rpx, rqt, rrvgo, Rsamtools, rScudo, rsemmed, rSWeeP, RTCGAToolbox, RTN, RTNduals, RTNsurvival, Rtpca, RUVSeq, RVS, rWikiPathways, S4Vectors, samExploreR, sampleClassifier, sampleClassifierData, sangerseqR, satuRn, ScaledMatrix, scater, scCB2, scClassify, scDblFinder, scDD, scds, scFeatureFilter, SCLCBam, scMerge, SCnorm, scone, scoreInvHap, scp, scPCA, scpdata, scran, scRepertoire, scRNAseq, scruff, scuttle, sechm, segmentSeq, selectKSigs, seqCAT, SeqGate, seqLogo, seqPattern, seqplots, seqsetvis, SeqSQC, sequencing, SeqVarTools, sesame, SEtools, sevenC, SGSeq, SharedObject, shinyMethyl, ShortRead, SIAMCAT, SigCheck, SigFuge, signatureSearch, SigsPack, SimBenchData, SIMD, SimFFPE, similaRpeak, SIMLR, simulatorZ, sincell, Single.mTEC.Transcriptomes, SingleCellExperiment, SingleCellMultiModal, singleCellTK, SingleR, SingscoreAMLMutations, sitePath, slingshot, slinky, SMAD, snapcount, snifter, SNPediaR, SNPhood, SNPhoodData, soGGi, sojourner, SOMNiBUS, sparseDOSSA, sparseMatrixStats, sparsenetgls, SparseSignatures, SpatialCPie, SpatialExperiment, spatialHeatmap, spatialLIBD, specL, Spectra, SpectralTAD, spicyR, SpidermiR, splatter, SPLINTER, splots, spqn, SPsimSeq, sRACIPE, srnadiff, SSPA, stageR, STAN, StarBioTrek, STATegRa, statTarget, STexampleData, strandCheckR, struct, Structstrings, structToolbox, SubCellBarCode, SummarizedBenchmark, SummarizedExperiment, sva, swfdr, switchde, synapter, SynExtend, systemPipeR, systemPipeRdata, systemPipeShiny, systemPipeTools, TabulaMurisData, TADCompare, TargetSearch, tartare, TBSignatureProfiler, TCGAbiolinks, TCGAbiolinksGUI, TCGAbiolinksGUI.data, TCGAutils, TENxBrainData, TENxBUSData, TENxPBMCData, TENxVisiumData, TFARM, TFBSTools, TFHAZ, TFutils, tidybulk, tidySingleCellExperiment, tidySummarizedExperiment, tigre, TileDBArray, timecoursedata, timeOmics, TimerQuant, tissueTreg, TMExplorer, TMixClust, TOAST, tomoda, ToPASeq, topconfects, topdownr, ToxicoGx, TPP, tracktables, trackViewer, TrajectoryUtils, transcriptogramer, transcriptR, transomics2cytoscape, TraRe, traseR, Travel, TreeAndLeaf, treekoR, TreeSummarizedExperiment, Trendy, tricycle, tRNA, tRNAdbImport, tRNAscanImport, TRONCO, TTMap, TurboNorm, TVTB, twoddpcr, Ularcirc, UMI4Cats, uncoverappLib, UniProt.ws, variancePartition, VariantAnnotation, VariantFiltering, variants, VariantToolsData, VCFArray, velociraptor, VERSO, vidger, ViSEAGO, vissE, vsn, wavClusteR, weitrix, wpm, XBSeq, xcms, Xeva, XNAString, yamss, YAPSA, zebrafishRNASeq, zellkonverter, zinbwave
Links To Me
Build Report Build Report

Package Archives

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

Source Package BiocStyle_2.20.2.tar.gz
Windows Binary BiocStyle_2.20.2.zip
macOS 10.13 (High Sierra) BiocStyle_2.20.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocStyle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocStyle
Bioc Package Browser https://code.bioconductor.org/browse/BiocStyle/
Package Short Url https://bioconductor.org/packages/BiocStyle/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive