Package: glyclean
Title: Perform Preprocessing on Glycomics and Glycoproteomics Data
Version: 0.16.0
Authors@R: 
    person("Bin", "Fu", , "23110220018@m.fudan.edu.cn", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8567-2997"))
Description: Provides comprehensive data preprocessing tools for
        glycomics and glycoproteomics experiments. The package offers
        both automated and manual preprocessing pipelines, including
        normalization (median, quantile, vsn, total area), missing
        value handling (filtering, imputation using various methods),
        batch effect correction (using ComBat and other methods), data
        aggregation (at peptide, glycan, or site level), and quality
        control functions. The automated pipeline intelligently selects
        appropriate methods based on data characteristics and sample
        size, making it easy to prepare clean, analysis-ready data for
        downstream statistical analysis within the glycoverse
        ecosystem. Works seamlessly with 'glyexp::GlycomicSE',
        'glyexp::GlycoproteomicSE', and
        'SummarizedExperiment::SummarizedExperiment' objects to ensure
        data consistency and interoperability.
License: MIT + file LICENSE
Suggests: testthat (>= 3.2.0), vdiffr, glyread (>= 0.6.2), glyrepr (>=
        0.7.4), vsn, impute, MASS, knitr, rmarkdown, pheatmap,
        ggplotify, factoextra, patchwork, compositions
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://glycoverse.github.io/glyclean/
Imports: checkmate, cli, dplyr, glyexp (>= 0.16.0), lifecycle, limma,
        magrittr, matrixStats, missForest, pcaMethods, purrr, rlang,
        seqinr, stringr, tidyr, tibble, tidyselect, UniProt.ws, withr,
        forcats, stats, ggplot2, sva, SummarizedExperiment, S4Vectors,
        methods
Depends: R (>= 4.1)
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev libicu-dev libpng-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://glycoverse.r-universe.dev
Date/Publication: 2026-10-15 17:29:57 UTC
RemoteUrl: https://github.com/glycoverse/glyclean
RemoteRef: v0.16.0
RemoteSha: 92a1368ff8310eae00738122b652b917aca405f8
NeedsCompilation: no
Packaged: 2026-10-16 08:29:51 UTC; root
Author: Bin Fu [aut, cre] (ORCID: <https://orcid.org/0000-0001-8567-2997>)
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>