Package: glysmith
Title: Full-Featured Analysis Pipeline for Glycomics and
        Glycoproteomics
Version: 0.12.3
Authors@R: 
    person("Bin", "Fu", , "23110220018@m.fudan.edu.cn", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0001-8567-2997"))
Description: glysmith provides high-level, end-to-end workflows for
        glycomics and glycoproteomics data analysis within the
        glycoverse ecosystem. It acts as an orchestrator that
        integrates data cleaning, quality control, derived trait
        computation, motif detection, statistical testing, and
        visualization into unified, one-command analytical pipelines.
        Featuring AI-assisted pipeline generation, glysmith can
        intelligently translate natural language research questions
        into executable analysis blueprints, streamlining complex
        bioinformatics workflows. Built on top of the 'GlycomicSE' and
        'GlycoproteomicSE' data containers and domain-knowledge-aware
        infrastructure provided by glyclean, glydet, glymotif,
        glystats, glyvis, and related packages, glysmith enables users
        to quickly forge polished tables, figures, and analysis reports
        suitable for publication. The package is designed for
        reproducibility and ease of use, allowing both novice and
        advanced users to obtain standardized and structure-aware
        results with minimal code while retaining full flexibility for
        customization.
License: MIT + file LICENSE
Suggests: glyclean (>= 0.10.1), glyanno (>= 0.6.1), glydb (>= 0.4.0),
        glydet (>= 0.10.1), glyfun (>= 0.1.0), glyrepr (>= 1.0.0),
        glystats (>= 0.6.2), glyvis (>= 0.5.0), glymotif (>= 0.19.0),
        knitr, withr, pROC, Rtsne, uwot, EnhancedVolcano, enrichplot,
        org.Hs.eg.db, clusterProfiler, ReactomePA, ggplotify, pheatmap,
        factoextra, FSA, ggseqlogo, missForest, Hmisc, GGally,
        survival, UniProt.ws, ropls, testthat (>= 3.0.0)
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://glycoverse.github.io/glysmith/
Imports: checkmate, cli, ellmer, dplyr, fs, ggplot2, glyexp (>=
        0.16.0), glue, jsonlite, methods, purrr, readr, rlang,
        rmarkdown, S4Vectors, stringr, SummarizedExperiment, tibble
Depends: R (>= 4.1.0)
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://glycoverse.r-universe.dev
Date/Publication: 2026-08-26 02:26:35 UTC
RemoteUrl: https://github.com/glycoverse/glysmith
RemoteRef: v0.12.3
RemoteSha: be7c1e761f03bd0920e0d7dc8fda6c427b4c266c
NeedsCompilation: no
Packaged: 2026-10-16 08:30:51 UTC; root
Author: Bin Fu [aut, cre, cph] (ORCID: <https://orcid.org/0000-0001-8567-2997>)
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>