BiocStyle

DOI: 10.18129/B9.bioc.BiocStyle    

This is the development version of BiocStyle; for the stable release version, see BiocStyle.

Standard styles for vignettes and other Bioconductor documents

Bioconductor version: Development (3.9)

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

Author: Andrzej OleĊ›, 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", version = "3.9")

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 2.11.0
In Bioconductor since BioC 2.13 (R-3.0) (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 chipseqDB, curatedBreastData, methylationArrayAnalysis, rnaseqGene, simpleSingleCell
Imports Me abseqR, ASpli, BiocWorkflowTools, BPRMeth, BubbleTree, chimeraviz, COMPASS, cytofWorkflow, geneXtendeR, PathoStat, regionReport, Rmmquant, Rqc, srnadiff
Suggests Me ABAData, ABAEnrichment, ACE, adaptest, AffiXcan, affycoretools, AHEnsDbs, AllelicImbalance, allenpvc, AMOUNTAIN, amplican, AneuFinder, annotation, AnnotationDbi, AnnotationFilter, AnnotationForge, AnnotationHub, AnnotationHubData, annotatr, anota2seq, arrayQualityMetrics, arrays, artMS, ASGSCA, ASICS, ASICSdata, AssessORF, AssessORFData, ASSIGN, ATACseqQC, AUCell, BaalChIP, bacon, bamsignals, basecallQC, BASiCS, BayesPeak, bayNorm, baySeq, beachmat, beadarray, BeadDataPackR, BEARscc, BgeeDB, bigmelon, bigmemoryExtras, bioassayR, bioCancer, BiocFileCache, BiocMetaWorkflow, BiocNeighbors, BiocOncoTK, BioCor, BiocParallel, biomaRt, biomformat, biosigner, biotmle, BitSeq, blima, blimaTestingData, BloodCancerMultiOmics2017, bnbc, branchpointer, breakpointR, breakpointRdata, BridgeDbR, BrowserViz, bsseq, BUMHMM, BUScorrect, CAFE, CAGEfightR, CAGEr, CAMTHC, CancerInSilico, CAnD, Cardinal, CardinalWorkflows, CATALYST, cbaf, ccfindR, ccrepe, cellbaseR, cellity, CellMapper, CellMapperData, cellTree, CexoR, ChemmineDrugs, ChemmineOB, ChemmineR, Chicago, ChIPComp, chipenrich, chipenrich.data, ChIPexoQual, ChIPpeakAnno, ChIPQC, ChIPseeker, ChIPSeqSpike, chromstaR, chromswitch, ClassifyR, cleanUpdTSeq, cleaver, clipper, CLLmethylation, clusterSeq, ClusterSignificance, CNEr, CNPBayes, COCOA, CoGAPS, compcodeR, condcomp, CONFESS, consensusSeekeR, contiBAIT, conumee, CopyhelpeR, CopyNeutralIMA, CopywriteR, coRdon, CoRegNet, COSMIC.67, cosmiq, CountClust, covRNA, cpvSNP, CRISPRseek, CrispRVariants, CTDquerier, ctsGE, curatedBladderData, curatedCRCData, curatedMetagenomicData, curatedOvarianData, curatedTCGAData, CVE, cydar, dada2, dagLogo, DaMiRseq, DAPAR, DChIPRep, ddPCRclust, decontam, DEFormats, DEGreport, DelayedArray, DelayedMatrixStats, DEP, DEqMS, derfinder, derfinderHelper, derfinderPlot, DEScan2, DEXSeq, DiffBind, diffcyt, diffuStats, discordant, DmelSGI, dmrseq, DNABarcodes, doppelgangR, Doscheda, DOSE, drawProteins, DRIMSeq, DropletUtils, 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, EventPointer, ExperimentHub, ExperimentHubData, ExpressionNormalizationWorkflow, FamAgg, FastqCleaner, fCCAC, fCI, FELLA, FindMyFriends, flowcatchR, flowMap, FlowSOM, fmcsR, FourCSeq, furrowSeg, GA4GHclient, GA4GHshiny, GARS, gcapc, GDSArray, genbankr, GeneAccord, genefilter, GeneOverlap, geneplast, generegulation, GeneStructureTools, GenoGAM, GenomeInfoDb, GenomicAlignments, GenomicDataCommons, GenomicFeatures, GenomicFiles, GenomicInteractions, GenomicRanges, GenomicScores, GenomicTuples, genoset, GenVisR, GeuvadisTranscriptExpr, ggbio, Glimma, glmSparseNet, GMRP, GOexpress, GOfuncR, GOpro, goSTAG, gpart, gQTLBase, gQTLstats, graphite, GreyListChIP, GRmetrics, groHMM, GSAR, GSE62944, GSEABase, GSEABenchmarkeR, GUIDEseq, Gviz, gwasurvivr, Harman, HarmanData, HD2013SGI, HDCytoData, HDF5Array, HelloRanges, HelloRangesData, highthroughputassays, Hiiragi2013, hipathia, HIREewas, HiTC, HMP16SData, HPAanalyze, hpar, HTSFilter, HumanAffyData, ideal, iGC, igvR, IHW, IHWpaper, illuminaio, imageHTS, IMAS, Imetagene, immunoClust, InPAS, INSPEcT, InTAD, InteractionSet, InterMineR, IONiseR, IRanges, iSEE, isomiRs, IVAS, JctSeqData, JunctionSeq, karyoploteR, kissDE, liftOver, Linnorm, loci2path, Logolas, LOLA, LoomExperiment, LowMACA, lpsymphony, LRBaseDbi, M3D, MACPET, maEndToEnd, MAGeCKFlute, mAPKL, maser, MatrixRider, matter, MaxContrastProjection, MBASED, MBttest, MCbiclust, mCSEA, mCSEAdata, mdgsa, MEAL, MEDIPS, messina, MetaboSignal, metagene, metagenomeFeatures, metavizr, methimpute, methInheritSim, MethPed, MethylAid, MethylAidData, methylInheritance, MethylMix, methyvim, methyvimData, MetNet, mfa, microbiome, mimager, minfi, minionSummaryData, MIRA, miRcomp, miRmine, miRSM, miRsponge, missMethyl, missRows, mixOmics, mlm4omics, MLSeq, MMDiff2, MODA, mogsa, MoonlightR, motifbreakR, motifStack, mpra, MSnbase, MSnID, msPurity, msqc1, MSstats, MSstatsBioData, MSstatsTMT, MTseeker, MultiAssayExperiment, MultiDataSet, multiHiCcompare, multiMiR, MutationalPatterns, MWASTools, mygene, myvariant, mzR, NADfinder, NanoStringDiff, NanoStringQCPro, NarrowPeaks, ndexr, netbiov, nethet, netprioR, netReg, nondetects, normr, npGSEA, nucleoSim, nucleR, oligo, omicade4, omicRexposome, OmicsMarkeR, omicsPrint, Onassis, OnassisJavaLibs, OncoScore, OncoSimulR, ontoProc, OPWeight, ORFik, Organism.dplyr, Oscope, OUTRIDER, PAA, PANTHER.db, PanVizGenerator, parathyroidSE, pasilla, PasillaTranscriptExpr, Path2PPI, paxtoolsr, Pbase, pcaExplorer, PCAN, PCHiCdata, PepsNMR, PepsNMRData, perturbatr, phantasus, phenopath, philr, phyloseq, Pi, Pigengene, plethy, plotGrouper, plyranges, Polyfit, powerTCR, pqsfinder, profileScoreDist, pRoloc, pRolocGUI, PROPER, Prostar, proteomics, ProteomicsAnnotationHubData, ProteoMM, PSEA, PureCN, PWMEnrich, qcmetrics, QDNAseq, qpgraph, qsea, QSutils, quantro, QuasR, R3CPET, RaggedExperiment, rain, ramwas, RandomWalkRestartMH, Rbowtie, Rcade, rcellminer, rcellminerData, rCGH, RcisTarget, RCy3, RCyjs, rDGIdb, ReactomePA, recount, recountWorkflow, recoup, RedeR, RefNet, regioneR, regsplice, ReQON, restfulSE, rexposome, rfPred, RGMQL, RGMQLlib, RGraph2js, RGSEA, rhdf5, rhdf5client, Rhdf5lib, Rhtslib, RiboProfiling, riboSeqR, RIVER, RJMCMCNucleosomes, RNAprobR, RNAseq123, rnaseqcomp, RnaSeqSampleSize, RnaSeqSampleSizeData, Rnits, rols, ropls, rpx, rqt, Rsamtools, RTCGAToolbox, RTN, RTNduals, RTNsurvival, RUVcorr, RUVSeq, RVS, rWikiPathways, S4Vectors, samExploreR, sampleClassifier, sampleClassifierData, sangerseqR, scater, scDD, SCLCBam, SCnorm, scone, scoreInvHap, scran, scRNAseq, scruff, segmentSeq, seqCAT, seqPattern, seqplots, seqsetvis, SeqSQC, sequencing, SeqVarTools, sevenC, SGSeq, shinyMethyl, ShortRead, SIAMCAT, SigCheck, SigFuge, signet, SIMD, similaRpeak, SIMLR, simulatorZ, sincell, Single.mTEC.Transcriptomes, SingleCellExperiment, singleCellTK, slinky, SNPediaR, SNPhood, SNPhoodData, soGGi, sparseDOSSA, sparsenetgls, SparseSignatures, specL, SpidermiR, splatter, SPLINTER, SSPA, stageR, STAN, StarBioTrek, STATegRa, statTarget, strandCheckR, SummarizedBenchmark, SummarizedExperiment, sva, SVAPLSseq, swfdr, switchde, synapter, systemPipeR, systemPipeRdata, TabulaMurisData, TargetSearch, TCGAbiolinks, TCGAbiolinksGUI, TCGAbiolinksGUI.data, TCGAutils, TENxBrainData, TENxPBMCData, TFARM, TFBSTools, TFHAZ, TFutils, tigre, TimerQuant, tissueTreg, TMixClust, ToPASeq, topdownr, TPP, tracktables, trackViewer, transcriptogramer, transcriptR, traseR, Trendy, tRNA, tRNAdbImport, tRNAscanImport, TRONCO, TTMap, TurboNorm, TVTB, twoddpcr, universalmotif, variancePartition, VariantAnnotation, VariantFiltering, variants, VariantToolsData, vidger, vsn, wavClusteR, XBSeq, xcms, yamss, yriMulti, zebrafishRNASeq, zinbwave
Links To Me
Build Report  

Package Archives

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

Source Package BiocStyle_2.11.0.tar.gz
Windows Binary BiocStyle_2.11.0.zip
Mac OS X 10.11 (El Capitan) BiocStyle_2.11.0.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 http://bioconductor.org/packages/BiocStyle/
Package Downloads Report Download Stats

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