Package: omiprep 1.0.0

David Hughes

omiprep: Omics 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. Formerly known as metaboprep.

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

omiprep_1.0.0.tar.gz
omiprep_1.0.0.zip(r-4.7)omiprep_1.0.0.zip(r-4.6)omiprep_1.0.0.zip(r-4.5)
omiprep_1.0.0.tgz(r-4.6-any)omiprep_1.0.0.tgz(r-4.5-any)
omiprep_1.0.0.tar.gz(r-4.7-any)omiprep_1.0.0.tar.gz(r-4.6-any)
omiprep_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
omiprep/json (API)

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

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

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

On CRAN:

Conda:

5.94 score 16 scripts 38 exports 149 dependencies

Last updated from:6994838d7f. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK232
source / vignettesOK386
linux-release-x86_64OK250
macos-release-arm64OK164
macos-oldrel-arm64OK185
windows-develOK211
windows-releaseOK189
windows-oldrelOK208
wasm-releaseOK194

Exports:add_layeravailable_data_formatsavailable_report_templatesbatch_normaliseclean_namescontinuous_power_plotcramerVeval.power.binary.imbalancedeval.power.contexportexport_cometsexport_metaboanalystexport_omiprepfeature_describefeature_skewnessfeature_summaryfind.cont.effect.sizes.2.simfind.PA.effect.sizes.2.simgenerate_reportimbalanced_power_plotmissingnessmultivariate_anovaOmiprepoutlier_detectionoutlierspc_and_outliersquality_controlread_metabolonread_nightingaleread_olinkread_somalogicrun_metaboprep1sample_summaryshiny_appsummarisetotal_sum_abundancetree_and_independent_featuresvariable_by_factor

Dependencies:abindarrowaskpassassertthatbackportsbase64encBiobaseBiocGenericsbitbit64blobbootbroombslibcachemcarcarDatacellrangerclicolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDerivdigestdoBydplyrDTduckdbevaluatefarverfastmapfontawesomeforcatsforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifglueGPArotationgridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrirlbaisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamnormtmodelrnFactorsnlmenloptrnnetnumDerivOlinkAnalyzeopensslopenxlsxotelpbkrtestpcaMethodspillarpkgconfigplotlyplyrpolynomprettyunitsprogresspromisespsychpurrrpwrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadxlreformulasrematchreshape2rlangrmarkdownrstatixS7sassscalesshinyshinycssloadersSomaDataIOsourcetoolsSparseMstringistringrsurvivalsystibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunxtableyamlzipzoo

Batch Normalise

Rendered frombatch_normalise.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-04-19
Started: 2025-06-04

Export Data

Rendered fromexport.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-04-19
Started: 2025-06-26

Feature summary

Rendered fromfeature_summary.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-04-19
Started: 2025-06-10

Generate QC Report

Rendered fromgenerate_report.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-11
Started: 2025-06-05

Import Metabolon Metabolomic Data

Rendered frommetabolon.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-11
Started: 2025-06-26

Import Nightingale Metabolomic Data

Rendered fromnightingale.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-11
Started: 2025-06-26

Import Olink Proteomic Data

Rendered fromolink.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-11
Started: 2025-06-25

Import Somalogic Proteomic Data

Rendered fromsomalogic.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-11
Started: 2025-06-26

quality_control

Rendered fromquality_control.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-11
Started: 2025-06-26

Sample summary

Rendered fromsample_summary.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-04-19
Started: 2025-06-04

Skewness-Based Feature QC

Rendered fromskewness_qc.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-11
Started: 2026-04-13

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
Omiprep Objectclass_omiprep Omiprep
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 Omiprep Objectexport
Export Data to `COMETS` formatexport_comets
Export Data to `MetaboAnalyst` formatexport_metaboanalyst
Export Data to `Omiprep` formatexport_omiprep
Summary Statistics for Featuresfeature_describe
Estimate Feature Skewnessfeature_skewness
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
Omics 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
Omiprep Shiny Appshiny_app
Summary Statisticssummarise
Summary Method for Omiprep Objectsummary summary.Omiprep
Estimates total sum abundancetotal_sum_abundance
Identify Independent Features in a Numeric Matrixtree_and_independent_features
ggplot2 violin plotvariable_by_factor