BiocStyle

DOI: 10.18129/B9.bioc.BiocStyle    

Standard styles for vignettes and other Bioconductor documents

Bioconductor version: Release (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 (!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 2.20.2
In Bioconductor since BioC 2.13 (R-3.0) (8 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, methylationArrayAnalysis, org.Mxanthus.db, Pigengene, rnaseqGene, RnaSeqGeneEdgeRQL, sangeranalyseR
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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, 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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
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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
Package Short Url https://bioconductor.org/packages/BiocStyle/
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