Changes in version 1.3.2                        

SIGNIFICANT USER-VISIBLE CHANGES

  - The link provided inside connect_database() has been updated in
    order to connect with the latest version of regulonDB v10.8.

                        Changes in version 1.3.1                        

BUG FIXES

  - Fixed URL for the database. Resolves
    https://github.com/ComunidadBioInfo/regutools/issues/33.

                        Changes in version 1.1.3                        

SIGNIFICANT USER-VISIBLE CHANGES

  - The package CITATION file has been updated now that the online paper
    on regutools is available at
    https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa575/5861528
    with DOI 10.1093/bioinformatics/btaa575 and PMID: 32573705.

DOCUMENTATION UPDATES

  - roxygen version update was included and documentation was build
    under the new roxygen version.

                        Changes in version 1.1.1                        

SIGNIFICANT USER-VISIBLE CHANGES

  - The package CITATION file has been updated now that the pre-print on
    regutools is available at
    https://www.biorxiv.org/content/10.1101/2020.04.29.068551v1 with DOI
    https://doi.org/10.1101/2020.04.29.068551.

                       Changes in version 0.99.14                       

SIGNIFICANT USER-VISIBLE CHANGES

  - Now connect_database() as a bfc parameter instead of path.

                       Changes in version 0.99.13                       

SIGNIFICANT USER-VISIBLE CHANGES

  - Now connect_database() uses BiocFileCache::BiocFileCache() and
    BiocFileCache::bfcrpath() to download the database from Dropbox when
    it's not available from AnnotationHub::query() and caches the file
    so you don't have to re-download it multiple times.

                       Changes in version 0.99.12                       

SIGNIFICANT USER-VISIBLE CHANGES

  - Documentation website is now available at
    http://comunidadbioinfo.github.io/regutools/. It gets updated with
    every commit on the master branch (bioc-devel) using GitHub Actions
    and pkgdown.

                       Changes in version 0.99.11                       

BUG FIXES

  - Manual adjustment for lines > 80 chr in parameters description.

                       Changes in version 0.99.10                       

BUG FIXES

  - Bump Version to run R CMD check

                       Changes in version 0.99.9                        

BUG FIXES

  - Add a suggested biocView Transcription.

                       Changes in version 0.99.8                        

BUG FIXES

  - Change biocViews from AnnotationData to Software

                       Changes in version 0.99.7                        

BUG FIXES

  - Fix a bug in pkgdown that is currently resolved by Rscript -e
    'remotes::install_github("r-lib/pkgdown#1276")'. Details at
    https://github.com/r-lib/pkgdown/pull/1276 and related issues.

                       Changes in version 0.99.6                        

BUG FIXES

  - Manual adjust for some lines > 80 characters

                       Changes in version 0.99.5                        

BUG FIXES

  - Reindent lines and try line-wrapping for lines > 80 characters

                       Changes in version 0.99.4                        

NEW FEATURES

  - Added a NEWS.md file to track changes to the package.

                       Changes in version 0.99.3                        

SIGNIFICANT USER-VISIBLE CHANGES

  - DESCRIPTION file now contains an article-like summary in the field
    regutools package Description.
  - DESCRIPTION was updated to show only one maintainer as required by
    http://bioconductor.org/developers/package-guidelines/#description

BUG FIXES

  - Fix a bug in the function get_regulatory_network() related with
    Cytoscape conection.

                       Changes in version 0.99.2                        

SIGNIFICANT CHANGES

  - Removed the regutools.Rproj file (you can still have it, but it's
    not version controlled).
  - Bump R depends to 4.0 as required by BiocCheck. We'll see if it
    breaks.

                       Changes in version 0.99.1                        

BUG FIXES

  - Address as many errors, warnings and notes as possible from
    http://bioconductor.org/spb_reports/regutools_buildreport_20200302121040.html#malbec2_check_anchor.
    For the Windows error, it's likely related to mode = "w" versus mode
    = "wb" for utils::download.file() as in
    https://github.com/LieberInstitute/spatialLIBD/commit/7ac24dc72cc75e42c9af8382c661517f4a64f08d.

                       Changes in version 0.99.0                        

NEW FEATURES

  - Submitted to Bioconductor