# regutools 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. # regutools 1.3.1 BUG FIXES * Fixed URL for the database. Resolves https://github.com/ComunidadBioInfo/regutools/issues/33. # regutools 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. # regutools 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. # regutools 0.99.14 SIGNIFICANT USER-VISIBLE CHANGES * Now `connect_database()` as a `bfc` parameter instead of `path`. # regutools 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. # regutools 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. # regutools 0.99.11 BUG FIXES * Manual adjustment for lines > 80 chr in parameters description. # regutools 0.99.10 BUG FIXES * Bump Version to run R CMD check # regutools 0.99.9 BUG FIXES * Add a suggested biocView `Transcription`. # regutools 0.99.8 BUG FIXES * Change biocViews from AnnotationData to Software # regutools 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. # regutools 0.99.6 BUG FIXES * Manual adjust for some lines > 80 characters # regutools 0.99.5 BUG FIXES * Reindent lines and try line-wrapping for lines > 80 characters # regutools 0.99.4 NEW FEATURES * Added a `NEWS.md` file to track changes to the package. # regutools 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. # regutools 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. # regutools 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. # regutools 0.99.0 NEW FEATURES * Submitted to Bioconductor