Package: metaboprep 1.0.1

David Hughes

metaboprep: Metabolomics data preparation and processing pipeline

| Reads in raw Metabolon, Nightingale Health, Olink, and SomaLogic xls sheets, or flat text files and aids in data preparation of all metabolomics & proteomics data sets.

Authors:Laura Corbin [aut], David Hughes [aut, cre], Nicholas Sunderland [aut], Matthew Lee [aut], Alec McKinlay [aut]

metaboprep_1.0.1.tar.gz
metaboprep_1.0.1.zip(r-4.7)metaboprep_1.0.1.zip(r-4.6)metaboprep_1.0.1.zip(r-4.5)
metaboprep_1.0.1.tgz(r-4.6-any)metaboprep_1.0.1.tgz(r-4.5-any)
metaboprep_1.0.1.tar.gz(r-4.7-any)metaboprep_1.0.1.tar.gz(r-4.6-any)
metaboprep_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
metaboprep/json (API)

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

Bug tracker:https://github.com/mrcieu/metaboprep/issues

Pkgdown/docs site:https://mrcieu.github.io

On CRAN:

Conda:

7.26 score 27 stars 21 scripts 37 exports 148 dependencies

Last updated from:91d1084d5d. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK229
source / vignettesOK326
linux-release-x86_64OK223
macos-release-arm64OK153
macos-oldrel-arm64OK147
windows-develOK150
windows-releaseOK148
windows-oldrelOK228
wasm-releaseOK173

Exports:add_layeravailable_data_formatsavailable_report_templatesbatch_normaliseclean_namescontinuous_power_plotcramerVeval.power.binary.imbalancedeval.power.contexportexport_cometsexport_metaboanalystexport_metaboprepfeature_describefeature_summaryfind.cont.effect.sizes.2.simfind.PA.effect.sizes.2.simgenerate_reportimbalanced_power_plotMetaboprepmissingnessmultivariate_anovaoutlier_detectionoutlierspc_and_outliersquality_controlread_metabolonread_nightingaleread_olinkread_somalogicrun_metaboprep1sample_summaryshiny_appsummarisetotal_peak_areatree_and_independent_featuresvariable_by_factor

Dependencies:abindarrowaskpassassertthatbackportsbase64encBiobaseBiocGenericsbitbit64blobbootbroombslibcachemcarcarDatacellrangerclicolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDerivdigestdoBydplyrDTduckdbevaluatefarverfastmapfontawesomeforcatsforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifglueGPArotationgridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamnormtmodelrnFactorsnlmenloptrnnetnumDerivOlinkAnalyzeopensslopenxlsxotelpbkrtestpcaMethodspillarpkgconfigplotlyplyrpolynomprettyunitsprogresspromisespsychpurrrpwrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadxlreformulasrematchreshape2rlangrmarkdownrstatixS7sassscalesshinyshinycssloadersSomaDataIOsourcetoolsSparseMstringistringrsurvivalsystibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunxtableyamlzipzoo

Batch Normalise

Rendered frombatch_normalise.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-11-11
Started: 2025-06-04

Export Data

Rendered fromexport.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-11-11
Started: 2025-06-26

Feature summary

Rendered fromfeature_summary.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-11-11
Started: 2025-06-10

Generate QC Report

Rendered fromgenerate_report.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-11-11
Started: 2025-06-05

Import Metabolon Metabolomic Data

Rendered frommetabolon.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-11-11
Started: 2025-06-26

Import Nightingale Metabolomic Data

Rendered fromnightingale.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-12-05
Started: 2025-06-26

Import Olink Proteomic Data

Rendered fromolink.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-11-11
Started: 2025-06-25

Import Somalogic Proteomic Data

Rendered fromsomalogic.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-11-11
Started: 2025-06-26

quality_control

Rendered fromquality_control.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-09-04
Started: 2025-06-26

Sample summary

Rendered fromsample_summary.Rmdusingknitr::rmarkdownon May 07 2026.

Last update: 2025-11-11
Started: 2025-06-04

Readme and manuals

Help Manual

Help pageTopics
Add a Layer of Data (internal use)add_layer
List Available Data Formatsavailable_data_formats
List Available Report Templatesavailable_report_templates
Batch Normalisationbatch_normalise
Metaboprep Objectclass_metaboprep Metaboprep
Standardize Column or Feature Namesclean_names
continuous trait power analysis plotcontinuous_power_plot
Cramer's V (phi)cramerV
Estimate power for a binary variable in an imbalanced designeval.power.binary.imbalanced
estimate power for continuous variableeval.power.cont
Export Data from a Metaboprep Objectexport
Export Data to `COMETS` formatexport_comets
Export Data to `MetaboAnalyst` formatexport_metaboanalyst
Export Data to `Metaboprep` formatexport_metaboprep
Summary Statistics for Featuresfeature_describe
Feature Summary Statisticsfeature_summary
identify continuos trait effect sizesfind.cont.effect.sizes.2.sim
identify effect sizesfind.PA.effect.sizes.2.sim
Generate Output Reportgenerate_report
binary trait imbalanced design power analysis plotimbalanced_power_plot
Estimate Missingnessmissingness
multivariate analysismultivariate_anova
Identify indexes of outliers in dataoutlier_detection
Identify Outliersoutliers
Principal Component Analysispc_and_outliers
Metabolite Quality Controlquality_control
Read Metabolon Dataread_metabolon
Read Nightingale Data (format 1)read_nightingale
Read and Process Olink NPX Data Fileread_olink
Read and Process SomaLogic adat fileread_somalogic
Metaboprep 1 pipelinerun_metaboprep1
Sample Summary Statisticssample_summary
Metaboprep Shiny Appshiny_app
Summary Statisticssummarise
Summary Method for Metaboprep Objectsummary.Metaboprep
Estimates total peak abundancetotal_peak_area
Identify Independent Features in a Numeric Matrixtree_and_independent_features
ggplot2 violin plotvariable_by_factor