Package: omiprep
Title: Omics data preparation and processing pipeline
Version: 1.0.0
Authors@R: c(person("Laura", "Corbin",        email = "laura.corbin@bristol.ac.uk",        role = c("aut")), 
             person("David", "Hughes",        email = "hughes.evoanth@gmail.com",          role = c("aut", "cre")),
             person("Nicholas", "Sunderland", email = "nicholas.sunderland@bristol.ac.uk", role = c("aut")),
             person("Matthew", "Lee",         email = "matthew.lee@bristol.ac.uk",         role = c("aut")),
             person("Alec", "McKinlay",       email = "am17168@bristol.ac.uk",             role = c("aut")))
Description: | 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.
Depends: R (>= 4.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
Imports: boot, car, cli, ggplot2, ggpubr, nFactors, pcaMethods, irlba,
        psych, pwr, readxl, rmarkdown, S7, yaml, OlinkAnalyze,
        SomaDataIO, reshape2, openxlsx, stringr, shiny,
        shinycssloaders, bslib, DT, plotly
Suggests: knitr, dendextend, kableExtra, remotes, testthat (>= 3.0.0),
        withr
Remotes:
URL: https://mrcieu.github.io/omiprep/
Collate: 'class_omiprep.R' 'batch_normalise.R' 'continous_power_plot.R'
        'cramer_v.R' 'export.R' 'feature_describe.R'
        'feature_skewness.R' 'feature_summary.R' 'generate_report.R'
        'imbalanced_power_plot.R' 'missingness.R'
        'multivariate_anova.R' 'outlier_detection.R'
        'pc_and_outliers.R' 'quality_control.R' 'read_metabolon.R'
        'read_nightingale.R' 'read_olink.R' 'read_somalogic.R'
        'run_metaboprep1.R' 'sample_summary.R' 'shiny_app.R'
        'summarise.R' 'summary_omiprep.R' 'total_sum_abundance.R'
        'tree_and_independent_features.R' 'utils.R'
        'variable_by_factor.R' 'zzz.R'
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0.9000
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://mrcieu.r-universe.dev
Date/Publication: 2026-06-25 03:00:55 UTC
RemoteUrl: https://github.com/MRCIEU/omiprep
RemoteRef: HEAD
RemoteSha: 9b7616ef0298fb0b781aa99c85c7c66fee990d0b
NeedsCompilation: no
Packaged: 2026-06-25 05:11:59 UTC; root
Author: Laura Corbin [aut],
  David Hughes [aut, cre],
  Nicholas Sunderland [aut],
  Matthew Lee [aut],
  Alec McKinlay [aut]
Maintainer: David Hughes <hughes.evoanth@gmail.com>