Package: regutools
Title: regutools: an R package for data extraction from RegulonDB
Version: 1.23.0
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: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev python3 xz-utils libzmq3-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:59:10 UTC
RemoteUrl: https://github.com/bioc/regutools
RemoteRef: HEAD
RemoteSha: a894ec8d3e443d93c8530e90be1dec6a075b7734
NeedsCompilation: no
Packaged: 2025-10-30 09:32:01 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>
Built: R 4.6.0; ; 2025-10-30 09:35:15 UTC; windows
