DESCRIPTION

Package: MSnSet.utils
Type: Package
Title: Miscellaneous Functions for Proteomics Data Analysis
Version: 0.1.0
Date: 2023-03-14
Encoding: UTF-8
Author: Vladislav Petyuk
Maintainer: Vladislav Petyuk <petyuk@gmail.com>
Description: A collection of customized functions used for
    proteomics dataset analysis. The functions are geared towards using
    MSnSet (or ExpressionSet) object as the key data container.
    The package contains customized heatmaps, color schemes,
    convenient nested linear models, machine learning utilities, etc.
License: Artistic-2.0
biocViews: Proteomics, MassSpectrometry
Depends:
    R (>= 3.5.0),
    MSnbase
Imports:
    Biobase,
    BiocGenerics,
    BiocParallel,
    Biostrings,
    Boruta,
    car,
    ComplexHeatmap,
    circlize,
    data.table, 
    doParallel,
    DOSE,
    dplyr,
    foreach,
    forcats,
    ggplot2,
    ggrepel, 
    glmnet,
    glue,
    gplots,
    grid,
    Heatplus,
    invgamma,
    iterators,
    limma,
    lme4,
    Matrix, 
    methods,
    outliers,
    parallel,
    purrr, 
    qvalue, 
    randomForest,
    reshape2, 
    rlang,
    ROCR,
    pROC,
    scales,
    stats,
    statmod,
    stringr,
    sva,
    tibble, 
    tidyr, 
    tidyselect,
    umap, 
    utils,
    varSelRF,
    WGCNA,
    xtable,
    FField,
    MSnID
Suggests:
    BiocStyle,
    biomaRt,
    clusterProfiler,
    e1071,
    enrichplot,
    ggforce,
    ggnewscale,
    GOstats,
    knitr,
    msmsTests,
    org.Hs.eg.db,
    qpdf,
    RColorBrewer, 
    ReactomePA,
    rmarkdown,
    UniProt.ws,
    viridis
Remotes: 
    github::cran/FField,
    github::PNNL-Comp-Mass-Spec/MSnID@pnnl-master
VignetteBuilder: knitr
RoxygenNote: 7.3.1