BiocStyle

DOI: 10.18129/B9.bioc.BiocStyle    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BiocStyle.

Standard styles for vignettes and other Bioconductor documents

Bioconductor version: 3.10

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

Author: Andrzej OleÅ›, Martin Morgan, Wolfgang Huber

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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 2.14.4
In Bioconductor since BioC 2.13 (R-3.0) (6.5 years)
License Artistic-2.0
Depends
Imports bookdown, knitr (>= 1.12), 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, methylationArrayAnalysis, org.Mxanthus.db, rnaseqGene
Imports Me abseqR, ASpli, BiocWorkflowTools, BPRMeth, BubbleTree, chimeraviz, COMPASS, deco, DiscoRhythm, geneXtendeR, Melissa, PathoStat, PhyloProfile, regionReport, Rmmquant, Rqc, scTensor, scTGIF, srnadiff
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breakpointRdata, brendaDb, BridgeDbR, BrowserViz, bsseq, BUMHMM, BUScorrect, BUSpaRse, CAFE, CAGEfightR, CAGEr, CAGEWorkflow, CAMTHC, CancerInSilico, CAnD, Cardinal, CardinalWorkflows, CATALYST, cbaf, ccfindR, ccrepe, celda, cellbaseR, CellBench, cellity, CellMapper, CellMapperData, CellMixS, cellTree, CexoR, ChemmineDrugs, ChemmineOB, ChemmineR, Chicago, ChIPComp, chipenrich, chipenrich.data, ChIPexoQual, ChIPpeakAnno, ChIPQC, chipseqDB, chipseqDBData, ChIPSeqSpike, chromstaR, chromswitch, ClassifyR, cleanUpdTSeq, cleaver, clipper, CLLmethylation, clusterExperiment, clusterSeq, ClusterSignificance, CNEr, CNVRanger, COCOA, CoGAPS, coMET, compcodeR, CONFESS, consensusOV, consensusSeekeR, contiBAIT, conumee, CopyhelpeR, CopyNeutralIMA, CopyNumberPlots, CopywriteR, coRdon, CoRegNet, COSMIC.67, cosmiq, CountClust, covRNA, cpvSNP, CRISPRseek, CrispRVariants, csaw, csawUsersGuide, CTDquerier, ctsGE, curatedBladderData, curatedCRCData, curatedMetagenomicData, curatedOvarianData, curatedTCGAData, CVE, cydar, cytofast, dada2, dagLogo, DaMiRseq, DAPAR, dcanr, DChIPRep, ddPCRclust, debCAM, decompTumor2Sig, decontam, DEFormats, DEGreport, DelayedArray, DelayedMatrixStats, DEP, DepecheR, depmap, DEqMS, derfinder, derfinderHelper, derfinderPlot, DEScan2, DEWSeq, DEXSeq, DiffBind, diffcyt, diffuStats, discordant, DmelSGI, dmrseq, DNABarcodeCompatibility, DNABarcodes, doppelgangR, Doscheda, doseR, drawProteins, DRIMSeq, DropletUtils, dSimer, DSS, DuoClustering2018, dupRadar, easyRNASeq, EBImage, EDASeq, EGSEA, EGSEA123, eiR, ELMER, ELMER.data, EmpiricalBrownsMethod, EnrichmentBrowser, ensembldb, EpiDISH, epivizr, epivizrChart, epivizrData, epivizrServer, epivizrStandalone, eQTL, erma, ERSSA, EuPathDB, evaluomeR, EventPointer, ExperimentHub, ExperimentHubData, ExpressionNormalizationWorkflow, FamAgg, FastqCleaner, fCCAC, fCI, fcScan, FELLA, FindMyFriends, flowcatchR, flowMap, FlowSOM, flowSpecs, flowSpy, fmcsR, FourCSeq, furrowSeg, GA4GHclient, GA4GHshiny, GARS, gcapc, 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InPAS, INSPEcT, InTAD, InteractionSet, InterMineR, IONiseR, IRanges, iSEE, isomiRs, IVAS, JctSeqData, JunctionSeq, karyoploteR, kissDE, ldblock, liftOver, LinkHD, Linnorm, lipidr, loci2path, Logolas, LOLA, LoomExperiment, LowMACA, lpsymphony, LRBaseDbi, M3D, MACPET, maEndToEnd, mAPKL, maser, MAST, MatrixRider, matter, MaxContrastProjection, MBASED, mbkmeans, MBttest, MCbiclust, mCSEA, mCSEAdata, mdgsa, MEAL, MEDIPS, messina, MetaboSignal, metagene, metagene2, metagenomeFeatures, metavizr, methimpute, methInheritSim, MethPed, MethylAid, MethylAidData, methylCC, methylInheritance, MethylMix, methyvim, methyvimData, MetNet, mfa, microbiome, mimager, minfi, minionSummaryData, MIRA, miRcomp, miRmine, miRSM, miRspongeR, missMethyl, missRows, mixOmics, mlm4omics, MLSeq, MMAPPR2, MMAPPR2data, MMDiff2, MMUPHin, MODA, Modstrings, mogsa, MoonlightR, MOSim, motifbreakR, motifStack, MouseGastrulationData, mpra, MSMB, MSnbase, MSnID, msPurity, msqc1, MSstats, MSstatsBioData, MSstatsSampleSize, MSstatsTMT, MTseeker, MultiAssayExperiment, MultiDataSet, multiHiCcompare, multiMiR, muscat, muscData, MutationalPatterns, MWASTools, mygene, myvariant, mzR, NADfinder, NanoStringDiff, NanoStringQCPro, nanotubes, NarrowPeaks, ncGTW, ndexr, NestLink, netbiov, nethet, NetPathMiner, netprioR, netReg, netSmooth, ngsReports, nondetects, NormalyzerDE, normr, npGSEA, nucleoSim, nucleR, oligo, omicade4, omicRexposome, OmicsMarkeR, omicsPrint, OmnipathR, Onassis, OnassisJavaLibs, OncoScore, OncoSimulR, ontoProc, OPWeight, ORFik, Organism.dplyr, Oscope, OUTRIDER, OVESEG, PAA, PAIRADISE, PANTHER.db, PanVizGenerator, parathyroidSE, parglms, pasilla, PasillaTranscriptExpr, Path2PPI, paxtoolsr, Pbase, pcaExplorer, PCAN, PCHiCdata, peakPantheR, PepsNMR, PepsNMRData, perturbatr, PGA, phantasus, phenopath, philr, phyloseq, Pi, piano, Pigengene, plethy, plotGrouper, plyranges, Polyfit, PoTRA, powerTCR, pqsfinder, pram, PrecisionTrialDrawer, PrInCE, profileplyr, profileScoreDist, projectR, pRoloc, pRolocGUI, PROPER, Prostar, proteomics, ProteomicsAnnotationHubData, ProteoMM, proteoQC, PSEA, PureCN, PWMEnrich, qcmetrics, QDNAseq, qpgraph, qsea, qsmooth, QSutils, Qtlizer, quantro, QuasR, R3CPET, RaggedExperiment, rain, ramwas, RandomWalkRestartMH, rat2302frmavecs, Rbowtie, Rcade, rcellminer, rcellminerData, rCGH, RcisTarget, Rcwl, RcwlPipelines, RCy3, RCyjs, rDGIdb, ReactomePA, recount, recountWorkflow, recoup, RedeR, RefNet, regioneR, regsplice, ReQON, restfulSE, rexposome, RforProteomics, rfPred, RGMQL, RGMQLlib, RGraph2js, RGSEA, rhdf5, rhdf5client, Rhdf5lib, Rhisat2, Rhtslib, RiboProfiling, riboSeqR, RIVER, RJMCMCNucleosomes, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.Data, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAprobR, RNAseq123, rnaseqcomp, RnaSeqSampleSize, RnaSeqSampleSizeData, Rnits, rols, ropls, rpx, rqt, Rsamtools, rScudo, RTCGAToolbox, RTN, RTNduals, RTNsurvival, RUVcorr, RUVSeq, RVS, rWikiPathways, S4Vectors, samExploreR, sampleClassifier, sampleClassifierData, sangerseqR, sapFinder, scater, scDblFinder, scDD, scds, SCLCBam, scMerge, SCnorm, scone, scoreInvHap, scPCA, scran, scRNAseq, scruff, segmentSeq, seqCAT, seqPattern, seqplots, seqsetvis, SeqSQC, sequencing, SeqVarTools, sesame, SEtools, sevenC, SGSeq, SharedObject, shinyMethyl, ShortRead, SIAMCAT, SigCheck, SigFuge, signatureSearch, signet, SigsPack, SIMD, similaRpeak, SIMLR, simpleSingleCell, simulatorZ, sincell, Single.mTEC.Transcriptomes, SingleCellExperiment, singleCellTK, SingleR, SingscoreAMLMutations, sitePath, slingshot, slinky, SMAD, SNPediaR, SNPhood, SNPhoodData, soGGi, sojourner, sparseDOSSA, sparsenetgls, SparseSignatures, SpatialCPie, specL, SpectralTAD, SpidermiR, splatter, SPLINTER, sRACIPE, SSPA, stageR, STAN, StarBioTrek, STATegRa, statTarget, strandCheckR, Structstrings, SubCellBarCode, SummarizedBenchmark, SummarizedExperiment, sva, SVAPLSseq, swfdr, switchde, synapter, systemPipeR, systemPipeRdata, TabulaMurisData, TargetSearch, tartare, TCGAbiolinks, TCGAbiolinksGUI, TCGAbiolinksGUI.data, TCGAutils, TENxBrainData, TENxBUSData, TENxPBMCData, TFARM, TFBSTools, TFHAZ, TFutils, tigre, TimerQuant, tissueTreg, TMixClust, TOAST, ToPASeq, topdownr, TPP, tracktables, trackViewer, transcriptogramer, transcriptR, traseR, TreeSummarizedExperiment, Trendy, tRNA, tRNAdbImport, tRNAscanImport, TRONCO, TTMap, TurboNorm, TVTB, twoddpcr, Ularcirc, UniProt.ws, variancePartition, VariantAnnotation, VariantFiltering, variants, VariantToolsData, VCFArray, vidger, ViSEAGO, vsn, wavClusteR, XBSeq, xcms, Xeva, yamss, YAPSA, yriMulti, zebrafishRNASeq, zinbwave
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package BiocStyle_2.14.4.tar.gz
Windows Binary BiocStyle_2.14.4.zip
Mac OS X 10.11 (El Capitan) BiocStyle_2.14.4.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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