Package: POMA
Title: Tools for Omics Data Analysis
Version: 1.20.0
Authors@R: 
    c(person(given = "Pol",
             family = "Castellano-Escuder",
             role = c("aut", "cre"),
             email = "polcaes@gmail.com",
             comment = c(ORCID = "0000-0001-6466-877X"))
             )
Description: The POMA package offers a comprehensive toolkit designed
        for omics data analysis, streamlining the process from initial
        visualization to final statistical analysis. Its primary goal
        is to simplify and unify the various steps involved in omics
        data processing, making it more accessible and manageable
        within a single, intuitive R package. Emphasizing on
        reproducibility and user-friendliness, POMA leverages the
        standardized SummarizedExperiment class from Bioconductor,
        ensuring seamless integration and compatibility with a wide
        array of Bioconductor tools. This approach guarantees maximum
        flexibility and replicability, making POMA an essential asset
        for researchers handling omics datasets. See
        https://github.com/pcastellanoescuder/POMAShiny. Paper:
        Castellano-Escuder et al. (2021)
        <doi:10.1371/journal.pcbi.1009148> for more details.
License: GPL-3
Encoding: UTF-8
LazyData: true
biocViews: BatchEffect, Classification, Clustering, DecisionTree,
        DimensionReduction, MultidimensionalScaling, Normalization,
        Preprocessing, PrincipalComponent, Regression, RNASeq,
        Software, StatisticalMethod, Visualization
Imports: broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, fgsea,
        FSA, ggcorrplot, ggplot2, ggrepel, glmnet, grid, impute,
        janitor, limma, lme4, magrittr, MASS, mixOmics, multcomp,
        msigdbr, purrr, randomForest, RankProd (>= 3.14), rlang,
        SummarizedExperiment, sva, tibble, tidyr, utils, uwot, vegan
Suggests: BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly,
        tidyverse, testthat (>= 2.3.2)
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.0)
VignetteBuilder: knitr
URL: https://github.com/pcastellanoescuder/POMA
BugReports: https://github.com/pcastellanoescuder/POMA/issues
Config/pak/sysreqs: cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev
        libgmp3-dev make libicu-dev libpng-dev libxml2-dev libmpfr-dev
        libgl1-mesa-dev libssl-dev perl zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:01:06 UTC
RemoteUrl: https://github.com/bioc/POMA
RemoteRef: RELEASE_3_22
RemoteSha: 49dcbbe3d10d4019794564a162e94251b9a8dda5
NeedsCompilation: no
Packaged: 2025-11-11 16:42:14 UTC; root
Author: Pol Castellano-Escuder [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6466-877X>)
Maintainer: Pol Castellano-Escuder <polcaes@gmail.com>
Built: R 4.5.2; ; 2025-11-11 16:49:34 UTC; windows
