DESCRIPTION

Package: OmicSelector
Type: Package
Title: OmicSelector - a package for biomarker selection based on high-throughput experiments. 
Version: 1.0.0
Author: Konrad Stawiski
Maintainer: Konrad Stawiski <konrad.stawiski@umed.lodz.pl>
Description: OmicSelector is package is the environment, docker-based application and R package for biomarker signature selection from high-throughput experiments. Initially developed for miRNA-seq. The package introduces automatic and structured feature selection with further benchmarking using multiple data mining methods, thus allow to find the most overfitting resiliant signature (set of featrues) that can be used in biomarker validation studies. E.g. this package can be used to find the set of miRNAs with the greatest biomarker potential based on miRNAs-seq. This set can be further validated in cheaper qPCR studies.
License: License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: 
    knitr,
    rmarkdown
VignetteBuilder: knitr
StagedInstall: yes
Imports: 
    dplyr,
    snow,
    remotes,
    devtools,
    ellipsis,
    BiocManager,
    plyr,
    tibble,
    tidyr,
    XML,
    epiDisplay,
    rsq,
    MASS,
    caret,
    tidyverse,
    xtable,
    pROC,
    ggplot2,
    DMwR,
    ROSE,
    gridExtra,
    gplots,
    stringr,
    data.table,
    doParallel,
    Boruta,
    spFSR,
    varSelRF,
    My.stepwise,
    psych,
    C50,
    randomForest,
    nnet,
    reticulate,
    stargazer,
    ggrepel,
    classInt,
    plotly,
    keras,
    cutpointr,
    naniar,
    visdat,
    imputeMissings,
    foreach,
    deepnet,
    calibrate,
    networkD3,
    VennDiagram,
    RSNNS,
    kernlab,
    car,
    PairedData,
    profileR,
    xgboost,
    kableExtra,
    curl,
    tidyselect,
    rJava,
    mice,
    MatchIt,
    cluster,
    Biobase,
    Biocomb,
    ComplexHeatmap,
    GDCRNATools,
    R.utils,
    TCGAbiolinks,
    VIM,
    circlize,
    edgeR,
    mgcv,
    party,
    rmarkdown,
    rpart,
    sva,
    devtools,
    nnet,
    klaR,
    ParBayesianOptimization,
    recipes,
    resample,
    mlbench
RoxygenNote: 7.2.0
Authors@R: c(
    person("Konrad", "Stawiski", , "konrad.stawiski@umed.lodz.pl", role = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-6550-3384")
    ),
    person("Marcin", "Kaszkowiak", role = "aut"))
BugReports: https://github.com/kstawiski/OmicSelector/issues
URL: https://biostat.umed.pl/OmicSelector/ 
biocViews: Software
Depends: 
    R (>= 2.10)