Package: regutools
Title: regutools: an R package for data extraction from RegulonDB
Version: 1.25.0
Date: 2021-11-15
Authors@R: c(
    person ("Joselyn", "Chavez", email =  "joselynchavezf@gmail.com",
        role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4974-4591")),
    person("Carmina", "Barberena-Jonas", email = "car.barjon@gmail.com",
        role = c("aut"), comment = c(ORCID = "0000-0001-7413-638X")),
    person(c("Jesus", "E."), "Sotelo-Fonseca", email = "jemilianosf@gmail.com",
        role = c("aut"), comment = c(ORCID = "0000-0003-1600-2396")),
    person("Jose", "Alquicira-Hernandez", email = "joseah@lcg.unam.mx",
        role = c("ctb"), comment = c(ORCID = "0000-0002-9049-7780")),
    person("Heladia", "Salgado", email = "heladia@ccg.unam.mx",
        role = c("ctb"), comment = c(ORCID = "0000-0002-3166-5801")),
    person("Leonardo", "Collado-Torres", role = c("aut"),
        email = "lcolladotor@gmail.com",
        comment = c(ORCID = "0000-0003-2140-308X")),
    person("Alejandro", "Reyes", email = "alejandro.reyes.ds@gmail.com",
        role = c("aut"), comment = c(ORCID = "0000-0001-8717-6612"))
    )
Description: RegulonDB has collected, harmonized and centralized data
        from hundreds of experiments for nearly two decades and is
        considered a point of reference for transcriptional regulation
        in Escherichia coli K12. Here, we present the regutools R
        package to facilitate programmatic access to RegulonDB data in
        computational biology. regutools provides researchers with the
        possibility of writing reproducible workflows with automated
        queries to RegulonDB. The regutools package serves as a bridge
        between RegulonDB data and the Bioconductor ecosystem by
        reusing the data structures and statistical methods powered by
        other Bioconductor packages. We demonstrate the integration of
        regutools with Bioconductor by analyzing transcription factor
        DNA binding sites and transcriptional regulatory networks from
        RegulonDB. We anticipate that regutools will serve as a useful
        building block in our progress to further our understanding of
        gene regulatory networks.
License: Artistic-2.0
Encoding: UTF-8
Depends: R (>= 4.0)
Imports: AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges,
        Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils,
        BiocFileCache
RoxygenNote: 7.1.1
Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo,
        testthat (>= 2.1.0), covr
URL: https://github.com/ComunidadBioInfo/regutools
BugReports: https://support.bioconductor.org/t/regutools
biocViews: GeneRegulation, GeneExpression, SystemsBiology,
        Network,NetworkInference,Visualization, Transcription
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        python3 xz-utils libzmq3-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:52:39 UTC
RemoteUrl: https://github.com/bioc/regutools
RemoteRef: HEAD
RemoteSha: 7f9073361976c8aed050c7498fee6c84285adfc7
NeedsCompilation: no
Packaged: 2026-07-04 06:31:33 UTC; root
Author: Joselyn Chavez [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4974-4591>),
  Carmina Barberena-Jonas [aut] (ORCID:
    <https://orcid.org/0000-0001-7413-638X>),
  Jesus E. Sotelo-Fonseca [aut] (ORCID:
    <https://orcid.org/0000-0003-1600-2396>),
  Jose Alquicira-Hernandez [ctb] (ORCID:
    <https://orcid.org/0000-0002-9049-7780>),
  Heladia Salgado [ctb] (ORCID: <https://orcid.org/0000-0002-3166-5801>),
  Leonardo Collado-Torres [aut] (ORCID:
    <https://orcid.org/0000-0003-2140-308X>),
  Alejandro Reyes [aut] (ORCID: <https://orcid.org/0000-0001-8717-6612>)
Maintainer: Joselyn Chavez <joselynchavezf@gmail.com>