Package: cTRAP
Title: Identification of candidate causal perturbations from
        differential gene expression data
Version: 1.30.0
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: 7.3.3
Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table,
        dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics,
        highcharter, htmltools, httr, limma, methods, parallel,
        pbapply, purrr, qs2, 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: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:49:00 UTC
RemoteUrl: https://github.com/bioc/cTRAP
RemoteRef: RELEASE_3_23
RemoteSha: 4dc94680c47c04c2cdb2f5986dc970d4ab0239a6
NeedsCompilation: no
Packaged: 2026-11-11 12:36:35 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>