DESCRIPTION

Package: cTRAP
Title: Identification of candidate causal perturbations from differential gene 
    expression data
Version: 1.20.1
Authors@R: c(
        person(c("Bernardo", "P."), "de Almeida", role="aut"),
        person("Nuno", "Saraiva-Agostinho",
            email="nunodanielagostinho@gmail.com", role=c("aut", "cre")),
        person(c("Nuno", "L."), "Barbosa-Morais", role=c("aut", "led")))
Description: Compare differential gene expression results with those from known
    cellular perturbations (such as gene knock-down, overexpression or small 
    molecules) derived from the Connectivity Map. Such analyses allow not only 
    to infer the molecular causes of the observed difference in gene expression 
    but also to identify small molecules that could drive or revert specific 
    transcriptomic alterations.
Depends: R (>= 4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews: DifferentialExpression, GeneExpression, RNASeq, Transcriptomics,
    Pathways, ImmunoOncology, GeneSetEnrichment
URL: https://nuno-agostinho.github.io/cTRAP,
    https://github.com/nuno-agostinho/cTRAP
BugReports: https://github.com/nuno-agostinho/cTRAP/issues
Suggests: 
    testthat,
    knitr,
    covr,
    rmarkdown,
    spelling,
    biomaRt,
    remotes
RoxygenNote: 7.3.1
Imports: AnnotationDbi,
    AnnotationHub,
    binr,
    cowplot,
    data.table,
    dplyr,
    DT,
    fastmatch,
    fgsea,
    ggplot2,
    ggrepel,
    graphics,
    highcharter,
    htmltools,
    httr,
    limma,
    methods,
    parallel,
    pbapply,
    purrr,
    qs,
    R.utils,
    readxl,
    reshape2,
    rhdf5,
    rlang,
    scales,
    shiny (>= 1.7.0),
    shinycssloaders,
    stats,
    tibble,
    tools,
    utils
VignetteBuilder: knitr
Language: en-GB
Collate: 
    'utils.R'
    'CMap.R'
    'ENCODE.R'
    'cTRAP-package.r'
    'cmapR_subset.R'
    'compare.R'
    'drugSensitivity.R'
    'drugSetEnrichment.R'
    'floweRy.R'
    'plots.R'
    'shinyInterface.R'
    'shinyInterface_session.R'