Package: Macarron 1.11.0

Sagun Maharjan

Macarron: Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets

Macarron is a workflow for the prioritization of potentially bioactive metabolites from metabolomics experiments. Prioritization integrates strengths of evidences of bioactivity such as covariation with a known metabolite, abundance relative to a known metabolite and association with an environmental or phenotypic indicator of bioactivity. Broadly, the workflow consists of stratified clustering of metabolic spectral features which co-vary in abundance in a condition, transfer of functional annotations, estimation of relative abundance and differential abundance analysis to identify associations between features and phenotype/condition.

Authors:Amrisha Bhosle [aut], Ludwig Geistlinger [aut], Sagun Maharjan [aut, cre]

Macarron_1.11.0.tar.gz
Macarron_1.11.0.zip(r-4.5)Macarron_1.11.0.zip(r-4.4)Macarron_1.11.0.zip(r-4.3)
Macarron_1.11.0.tgz(r-4.4-any)Macarron_1.11.0.tgz(r-4.3-any)
Macarron_1.11.0.tar.gz(r-4.5-noble)Macarron_1.11.0.tar.gz(r-4.4-noble)
Macarron_1.11.0.tgz(r-4.4-emscripten)Macarron_1.11.0.tgz(r-4.3-emscripten)
Macarron.pdf |Macarron.html
Macarron/json (API)
NEWS

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

Peer review:

On BioConductor:Macarron-1.11.0(bioc 3.21)Macarron-1.10.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencingmetabolomicscoveragefunctionalpredictionclustering

4.41 score 13 scripts 200 downloads 10 exports 193 dependencies

Last updated 3 months agofrom:60ff9333c1. Checks:1 OK, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKDec 29 2024
R-4.5-winWARNINGDec 31 2024
R-4.5-linuxWARNINGDec 29 2024
R-4.4-winWARNINGDec 31 2024
R-4.4-macWARNINGDec 29 2024
R-4.3-winWARNINGDec 31 2024
R-4.3-macWARNINGDec 29 2024

Exports:calAVAcalEScalQvaldecorateIDfindMacModMacarronmakeDisMatprepInputprioritizeshowBest

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHbiglmBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacaToolscheckmatechemometricsclasscliclustercodacodetoolscolorspacecowplotcplmcpp11crayoncurldata.tableDBIDelayedArrayDEoptimRDerivdigestdoBydoParalleldplyrdynamicTreeCute1071edgeRevaluatefansifarverfastclusterfastmapfffontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgetoptggplot2glmmTMBglmnetglueGO.dbGPArotationgplotsgridExtragtablegtoolshashhighrHmischtmlTablehtmltoolshtmlwidgetshttrimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlarslatticelifecyclelimmalme4lmerTestlocfitloggingMaaslin2magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoisemetagenomeSeqmgcvmicrobenchmarkmimeminqamnormtmodelrmunsellmvtnormnlmenloptrnnetnumDerivopenssloptparsepbapplypbkrtestpcaPPpermutepheatmappillarpkgconfigplogrplsplyrpngpreprocessCoreproxypsclpsychpurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2RJSONIOrlangrmarkdownrobustbaserpartRSQLiterstudioapiS4ArraysS4VectorssassscalesshapesnowsomSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexTMBtweedieUCSC.utilsutf8vctrsveganviridisviridisLiteWGCNAwithrWrenchxfunxml2XVectoryaml

Macarron User Manual

Rendered fromMacarron.Rmdusingknitr::rmarkdownon Dec 29 2024.

Last update: 2023-11-27
Started: 2023-11-27