DESCRIPTION

Package: vp.misc
Type: Package
Title: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis
Version: 0.1
Date: 2015-03-24
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, colorschemes,
    convienient nested linear models, machine learning utilities, etc.
License: Beerware
biocViews: Proteomics, MassSpectrometry
Depends:
    R (>= 2.10),
    MSnbase
Imports:
    parallel,
    Biostrings,
    Boruta,
    ROCR,
    doParallel,
    BiocParallel,
    plyr,
    dplyr,
    gplots,
    foreach,
    glmnet,
    iterators,
    randomForest,
    varSelRF,
    Biobase,
    Heatplus,
    ade4,
    made4,
    outliers,
    ggplot2,
    xtable,
    clusterProfiler,
    stringr,
    FField,
    sva,
    lme4,
    e1071,
    UniProt.ws,
    org.Hs.eg.db,
    biomaRt,
    GOstats,
    ReactomePA,
    BiocStyle,
    WGCNA,
    gelnet,
    multcomp,
    bnlearn,
    pracma,
    umap
VignetteBuilder: knitr
Suggests:
    knitr
RoxygenNote: 7.1.1