Package: benchdamic 1.11.0
benchdamic: Benchmark of differential abundance methods on microbiome data
Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.
Authors:
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benchdamic.pdf |benchdamic.html✨
benchdamic/json (API)
NEWS
# Install 'benchdamic' in R: |
install.packages('benchdamic', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mcalgaro93/benchdamic/issues
- microbial_metabolism - (Data) Microbial metabolism
- ps_plaque_16S -
- ps_stool_16S -
On BioConductor:benchdamic-1.11.0(bioc 3.20)benchdamic-1.10.0(bioc 3.19)
Last updated 2 months agofrom:be905b6ff4
Exports:addKnowledgeareaCATCATcheckNormalizationcreateColorscreateConcordancecreateEnrichmentcreateMockscreatePositivescreateSplitscreateTIECDA_ALDEx2DA_ANCOMDA_basicDA_corncobDA_dearseqDA_DESeq2DA_edgeRDA_limmaDA_lindaDA_Maaslin2DA_MASTDA_metagenomeSeqDA_mixMCDA_NOISeqDA_SeuratDA_ZicoSeqenrichmentTestextractDAextractStatisticsfitDMfitHURDLEfitModelsfitNBfitZIGfitZINBget_counts_metadatagetDAgetPositivesgetStatisticsiterative_orderingmeanDifferencesnorm_CSSnorm_DESeq2norm_edgeRnorm_TSSplotConcordanceplotContingencyplotEnrichmentplotFDRplotFPRplotKSplotLogPplotMDplotMutualFindingsplotPositivesplotQQplotRMSEprepareObservedRMSErunDArunMocksrunNormalizationsrunSplitsset_ALDEx2set_ANCOMset_basicset_corncobset_dearseqset_DESeq2set_edgeRset_limmaset_lindaset_Maaslin2set_MASTset_metagenomeSeqset_mixMCset_NOISeqset_Seuratset_ZicoSeqsetNormalizationsweights_ZINB
Dependencies:abindade4ALDEx2ANCOMBCannotateAnnotationDbiapeaskpassbackportsbase64encbeachmatbeeswarmBHbiglmBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularbiomformatBiostringsbitbit64bitopsblobblusterbootbroombslibcachemCairocallrcarcarDatacaToolscellrangercheckmatechemometricsclarabelclasscliclueclustercodacodetoolscolorspacecommonmarkCompQuadFormcorncobcorpcorcowplotcplmcpp11crayoncrosstalkcurlCVXRdata.tableDBIdearseqDECIPHERdecontamDelayedArrayDelayedMatrixStatsdeldirDEoptimRDerivdescDescToolsDESeq2detectseparationdigestdirectlabelsDirichletMultinomialdirmultdoBydoParalleldoRNGdotCall64dplyrdqrnge1071ECOSolveRedgeRellipseenergyevaluateExactexpmfansifarverfastDummiesfastmapfBasicsfitdistrplusFNNfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgetoptggbeeswarmggdendroggplot2ggrastrggrepelggridgesgldglmmTMBglmnetglobalsgluegmpgoftestgplotsgridExtragslgssgtablegtoolsGUniFrachashherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttricaigraphinlineinterpIRangesirlbaisobanditeratorsjaneaustenrjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlarslaterlatticelatticeExtralazyevalleidenlifecyclelimmalistenvlme4lmerTestlmomlmtestlocfitlogginglpSolvelpSolveAPIMaaslin2magrittrMASSMASTMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmediationmemoisemetagenomeSeqmgcvMGLMmiamicrobenchmarkMicrobiomeStatmimeminiUIminqamitoolsmixOmicsmodeestmodelrmultcompMultiAssayExperimentmulttestmunsellmvtnormNADAnlmenloptrnnetNOISeqnumDerivopensslopenxlsxoptparseosqpparallellypatchworkpbapplypbkrtestpcaPPpermutepheatmapphyloseqpillarpixmappkgbuildpkgconfigpkgloadplogrplotlyplsplyrpngpolyclipprettyunitsprocessxprogressprogressrpromisesproxypspsclpurrrquadprogquantregR.methodsS3R.ooR.utilsR6raggRANNrappdirsrARPACKrbibutilsrbiomRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppGSLRcppHNSWRcppMLRcppParallelRcppProgressRcppTOMLRcppZigguratRdpackreadxlregistryrematchreshape2reticulateRfastrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRmpfrrmutilrngtoolsrobustbaseROCRROIROI.plugin.lpsolverootSolverpartrprojrootRSpectraRSQLiterstudioapirsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscaterscattermorescssctransformscuttleSeuratSeuratObjectshapeshinySingleCellExperimentsitmoslamsnowSnowballCsoftImputesomsourcetoolsspspamSparseArraySparseMsparseMatrixStatsspatialspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstablestablediststatipstatmodstringistringrSummarizedExperimentsurveysurvivalsyssystemfontstensortextshapingTH.datatibbletidyrtidyselecttidytexttidytreetimeDatetimeSeriestinytexTMBtokenizerstreeioTreeSummarizedExperimenttruncnormtrusttweedieUCSC.utilsutf8uwotvctrsveganVGAMviporviridisviridisLitewithrWrenchxfunXMLxtableXVectoryamlyulab.utilszCompositionszinbwavezipzlibbioczoo
An introduction to benchdamic
Rendered fromintro.Rmd
usingknitr::rmarkdown
on Jun 30 2024.Last update: 2024-03-07
Started: 2021-01-29