Package: Macarron 1.17.0

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]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Macarron/json (API)

# Install 'Macarron' in R:

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

Datasets:

chem_taxonomy - Chemical taxonomy lookup table

On BioConductor:Macarron-1.17.0(bioc 3.24)Macarron-1.16.0(bioc 3.23)

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

sequencing metabolomics coverage functionalprediction clustering

4.35 score 15 scripts 10 exports 178 dependencies

Last updated from:9abb534c5e. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	223
linux-devel-x86_64	NOTE	867
source / vignettes	OK	537
linux-release-x86_64	NOTE	889
macos-release-arm64	NOTE	455
macos-oldrel-arm64	NOTE	648
windows-devel	NOTE	922
windows-release	NOTE	897
windows-oldrel	NOTE	855
wasm-release	OK	233

Exports:calAVA calES calQval decorateID findMacMod Macarron makeDisMat prepInput prioritize showBest

Dependencies:abind backports base64enc BH biglm Biobase BiocGenerics BiocParallel bit bitops boot broom bslib cachem car carData caTools checkmate chemometrics class cli cluster coda codetools colorspace cowplot cplm cpp11 data.table DBI DelayedArray DEoptimR Deriv digest doBy doParallel dplyr dynamicTreeCut e1071 edgeR evaluate farver fastcluster fastmap ff fontawesome foreach forecast foreign formatR Formula fracdiff fs futile.logger futile.options generics GenomicRanges ggplot2 glmmTMB glmnet glue GPArotation gplots gridExtra gtable gtools hash highr Hmisc htmlTable htmltools htmlwidgets impute IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r lars lattice lifecycle limma lme4 lmerTest lmtest locfit logging Maaslin2 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mclust memoise metagenomeSeq mgcv mime minqa mnormt modelr mvtnorm nlme nloptr nnet numDeriv optparse pbapply pbkrtest pcaPP permute pheatmap pillar pkgconfig pls plyr preprocessCore proxy pscl psych purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rmarkdown robustbase rpart rstudioapi S4Arrays S4Vectors S7 sandwich sass scales Seqinfo shape snow som SparseArray SparseM statmod stringi stringr SummarizedExperiment survival tibble tidyr tidyselect timeDate tinytex TMB tweedie urca utf8 vctrs vegan viridisLite WGCNA withr Wrench xfun XVector yaml zoo

Macarron User Manual

Rendered fromMacarron.Rmdusingknitr::rmarkdown

Last update: 2026-04-02
Started: 2023-11-27

Help page	Topics
Calculate abundance versus anchor (AVA) of metabolic features.	calAVA
Calculate effect size of differential abundance of metabolic features.	calES
Calculate q-value of differential abundance of metabolic features.	calQval
Chemical taxonomy lookup table	chem_taxonomy
Create a chemical taxonomy table for annotated metabolic features. Uses a pregenerated chemical taxonomy table shipped with the package to assign chemical subclass and class to annotated features.	decorateID
Cluster metabolic features based on covarying abundances into modules	findMacMod
Macarron	Macarron
Create a biweight midcorrelation (WGCNA::bicor()) based distance matrix.	makeDisMat
Create a SummarizedExperiment object	prepInput
Rank metabolic features and prioritize based on predicted bioactivity.	prioritize
View highly prioritized bioactives grouped by modules.	showBest

Package: Macarron 1.17.0

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

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