Package: zAMPExplorer 0.1.0

Sedreh Nassirnia

zAMPExplorer: zAMPExplorer: A Versatile Shiny App for Microbiota Profiling in Clinical Microbiology

A Shiny web application offering a user-friendly, accessible, and reproducible platform for downstream analysis of 16S rRNA-based metagenomics data. Key features include quality control visualizations (e.g., rarefaction curves), community composition plots, and statistical analyses for alpha- and beta-diversity. For deeper insights, the app incorporates community typing using Dirichlet multinomial modeling (DMM) and dynamically integrates metadata for sample stratification. This enables users to test microbial associations with clinical or experimental variables using redundancy analysis (RDA).

Authors:Sedreh Nassirnia [aut, cre], Violeta Castelo-Szekely [aut], Farid Chaabane [aut], Valentin Scherz [aut], Trestan Pillonel [aut], Gilbert Greub [aut], Claire Bertelli [aut]

zAMPExplorer_0.1.0.tar.gz
zAMPExplorer_0.1.0.zip(r-4.5)zAMPExplorer_0.1.0.zip(r-4.4)zAMPExplorer_0.1.0.zip(r-4.3)
zAMPExplorer_0.1.0.tgz(r-4.4-any)zAMPExplorer_0.1.0.tgz(r-4.3-any)
zAMPExplorer_0.1.0.tar.gz(r-4.5-noble)zAMPExplorer_0.1.0.tar.gz(r-4.4-noble)
zAMPExplorer_0.1.0.tgz(r-4.4-emscripten)zAMPExplorer_0.1.0.tgz(r-4.3-emscripten)
zAMPExplorer.pdf |zAMPExplorer.html✨
zAMPExplorer/json (API)

# Install 'zAMPExplorer' in R:
install.packages('zAMPExplorer', repos = c('https://metagenlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/metagenlab/zampexplorer/issues

On CRAN:

microbiologymetabarcodingvisualizationstatisticalmethod

2.60 score 1 scripts 1 exports 281 dependencies

Last updated 3 hours agofrom:8097e6084c. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-winWARNINGNov 11 2024
R-4.5-linuxWARNINGNov 23 2024
R-4.4-winWARNINGNov 11 2024
R-4.4-macWARNINGNov 23 2024
R-4.3-winWARNINGNov 23 2024
R-4.3-macWARNINGNov 23 2024

Exports:zAMPExplorer_app

Dependencies:abindade4apeaplotAsioHeadersaskpassbackportsbase64encbayesmbbmlebdsmatrixBHbiglmBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitopsbootbroombslibcacachemcallrcarcarDatacaToolscheckmatechemometricschromotecirclizeclasscliclisymbolsclueclustercodacodetoolscoincolorspacecolourpickercommonmarkComplexHeatmapComplexUpsetcompositionscowplotcplmcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDEoptimRDerivdigestDirichletMultinomialdoBydoParalleldoSNOWdplyrDTdtplyre1071edgeReulerrevaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGenSAgetoptGetoptLongggfunggiraphggnewscaleggplot2ggplotifyggrepelggsignifggstarggtreeggtreeExtraggvennglmmTMBglmnetGlobalOptionsgluegplotsgridExtragridGraphicsgtablegtoolshashherehighrHmischtmlTablehtmltoolshtmlwidgetshttpuvhttrigraphInteractiveComplexHeatmapIRangesisobanditeratorsjquerylibjsonlitekableExtraKernSmoothknitrlabelinglambda.rlarslaterlatticelazyevallibcoinlifecyclelimmalme4lmerTestlocfitloggingMaaslin2magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoisemetagenomeSeqmgcvMicEcomicrobenchmarkmicrobiomeMicrobiotaProcessmicroVizmimeminiUIminqamodelrmodeltoolsmultcompmulttestmunsellmvtnormnlmenloptrnnetnumDerivopenssloptparsepatchworkpbapplypbkrtestpcaPPpermutepheatmapphyloseqpicantepillarpixmappkgconfigplotlyplsplyrpngpolyclippolylabelrprocessxpromisesproxypspsclpurrrqapquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLRdpackreformulasregistryreshape2reticulaterhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrobustbaserpartrprojrootrstudioapiRtsneS4ArraysS4VectorssandwichsassscalesseriationshapeshinyshinydashboardshinyFilesshinyjsshinyWidgetsSingleCellExperimentsnowsomsourcetoolsspSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsvglitesyssystemfontstensorATH.datatibbletidyrtidyselecttidytreetinytexTMBtreeioTreeSummarizedExperimentTSPtweedieUCSC.utilsUpSetRutf8uuidvctrsveganVennDiagramviridisviridisLitewebshot2websocketwithrWrenchwritexlxfunxml2xtableXVectoryamlyulab.utilszlibbioczoo