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✨
DESCRIPTION
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:

7.52 score 28 stars 45 scripts 37 exports 147 dependencies

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

TargetResultTimeFilesSyslog
linux-devel-x86_64OK229
source / vignettesOK303
linux-release-x86_64OK237
macos-release-arm64OK170
macos-oldrel-arm64OK103
windows-develOK158
windows-releaseOK138
windows-oldrelOK147
wasm-releaseOK200

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.tableDBIdbplyrDerivdigestdoBydplyrDTduckdbevaluatefarverfastmapfontawesomeforcatsforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifglueGPArotationgridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmemoisemgcvmimeminqamnormtmodelrnFactorsnlmenloptrnnetnumDerivOlinkAnalyzeopensslopenxlsxotelpbkrtestpcaMethodspillarpkgconfigplotlyplyrpolynomprettyunitsprogresspromisespsychpurrrpwrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadxlreformulasrematchreshape2rlangrmarkdownrstatixS7sassscalesshinyshinycssloadersSomaDataIOsourcetoolsSparseMstringistringrsurvivalsystibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunxtableyamlzipzoo

Import Nightingale Metabolomic Data
Import Nightingale data directly into a Metaboprep object | Quick look at data structure of the imported data | QC Nightingale | Quick summary of the metaboprep object following QC
Rendered fromnightingale.Rmdusingknitr::rmarkdown

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

Import Somalogic Proteomic Data
Import SomaLogic data | Quick look to identify the types of data imported | Create Metaboprep object | Quick summary of the metaboprep object | QC Olink data | Quick summary of the metaboprep object following QC
Rendered fromsomalogic.Rmdusingknitr::rmarkdown

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

Sample summary
Create Metaboprep object | Summary of Metaboprep object | Run sample summary | Table of sample summary | Run sample summary on subset | Table of sample summary on subset | Run PCA analysis | Table of PCA analysis results | Additional attributes | Run sample & feature summaries together
Rendered fromsample_summary.Rmdusingknitr::rmarkdown

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

Feature summary
Create Metaboprep object | Summary of Metaboprep object | Run feature summary | Table of feature summary | Feature summary attributes | Run feature summary on subset | Table of feature summary for subset | Run sample & feature summaries together
Rendered fromfeature_summary.Rmdusingknitr::rmarkdown

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

Generate QC Report
Import example metabolomics data | Identify the Xenobiotics to exclude from the QC steps | QC the example Metabolon data | Generate the metaboprep report
Rendered fromgenerate_report.Rmdusingknitr::rmarkdown

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

Import Metabolon Metabolomic Data
Import Metabolon data | Quick look at data structure of the imported data | Create Metaboprep object | Quick summary of the metaboprep object | Identify the Xenobiotics to exclude from the QC steps | QC Metabolon | Quick summary of the metaboprep object following QC
Rendered frommetabolon.Rmdusingknitr::rmarkdown

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

Batch Normalise
Create Metaboprep object | Run batch normalisation | Accessing data | Raw input data | Batch normlalised data
Rendered frombatch_normalise.Rmdusingknitr::rmarkdown

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

Export Data
Setup | load the metaboprep library | Read in the data and make a Metaboprep object | Run the quality control | Export Metaboprep
Rendered fromexport.Rmdusingknitr::rmarkdown

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

Import Olink Proteomic Data
Import Olink data | Quick look to identify the types of data imported | Create Metaboprep object | Quick summary of the metaboprep object | QC Olink data | Quick summary of the metaboprep object following QC
Rendered fromolink.Rmdusingknitr::rmarkdown

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

quality_control
Run the quality control pipeline | View a summary of the Metaboprep object
Rendered fromquality_control.Rmdusingknitr::rmarkdown

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

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