Package: NADIA
Type: Package
Title: Missing Value-Aware Differential Abundance Analysis of DIA
        Proteomics Data
Version: 0.99.1
Authors@R: person(
    given = "Sergio",
    family = "Ciordia",
    email = "sciordia@gmail.com",
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-5726-853X"))
Description: Provides an end-to-end workflow for differential abundance
        analysis of protein quantification data, with particular
        attention to missing values in data-independent acquisition
        (DIA) proteomics. Quantification reports exported from
        Spectronaut, DIA-NN and Proteome Discoverer for TMT and
        label-free experiments (DDA/DIA) are converted into a common
        data structure, normalised, optionally batch-corrected, imputed
        and analysed using limma or limpa. The package includes
        individual and two-stage imputation strategies that treat
        values assumed to be missing at random and missing not at
        random separately. Data-driven functions evaluate and rank
        normalisation and imputation workflows using simulated
        missingness or spike-in datasets with known ground truth,
        allowing method selection to be justified for each dataset.
        Results can be explored through interactive Highcharts
        visualisations, static ggplot2 and ComplexHeatmap figures, and
        sortable tables.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/sciordia/NADIA,
        https://sciordia.github.io/NADIA/
BugReports: https://github.com/sciordia/NADIA/issues
biocViews: Software, Proteomics, MassSpectrometry,
        DifferentialExpression, Normalization, QualityControl,
        BatchEffect
Depends: R (>= 4.5.0)
Imports: dplyr, ggplot2, grDevices, grid, highcharter, htmltools,
        htmlwidgets, jsonlite, magrittr, methods, paletteer,
        RColorBrewer, reactable, readr, rlang, S4Vectors, stats,
        stringr, SummarizedExperiment, tibble, tidyr, tidyselect,
        tools, utils
Suggests: arrow, BERT, Biobase, BiocStyle, circlize, cluster,
        ComplexHeatmap, crosstalk, DBI, duckdb, e1071, ggsci, impute,
        imputeLCMD, knitr, limma, limpa, lme4, MASS, Mfuzz, mice,
        missForest, norm, pcaMethods, pROC, rmarkdown, rrcovNA, scales,
        testthat (>= 3.0.0), tidyHeatmap, vegan, viridis, vsn, withr
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Config/Needs/website: pkgdown
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-06 11:57:57 UTC
RemoteUrl: https://github.com/BiocStaging/NADIA
RemoteRef: HEAD
RemoteSha: c4a896085c0e2b7966e6ddf55af3f07aa3a4c114
NeedsCompilation: no
Packaged: 2026-10-06 12:07:17 UTC; root
Author: Sergio Ciordia [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5726-853X>)
Maintainer: Sergio Ciordia <sciordia@gmail.com>