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