Package: cTRAP
Title: Identification of candidate causal perturbations from
        differential gene expression data
Version: 1.28.0
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'
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:48:28 UTC
RemoteUrl: https://github.com/bioc/cTRAP
RemoteRef: RELEASE_3_22
RemoteSha: 216e3fc84c8820cc2f33c001be17577673c6c214
NeedsCompilation: no
Packaged: 2025-11-11 13:53:00 UTC; root
Author: Bernardo P. de Almeida [aut],
  Nuno Saraiva-Agostinho [aut, cre],
  Nuno L. Barbosa-Morais [aut, led]
Maintainer: Nuno Saraiva-Agostinho <nunodanielagostinho@gmail.com>
Built: R 4.5.2; ; 2025-11-11 13:59:17 UTC; windows
