NEWS
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