SIGNIFICANT USER-VISIBLE CHANGES
- Documentation website is now available at http://leekgroup.github.io/derfinderPlot/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.
SIGNIFICANT USER-VISIBLE CHANGES
- Code in all examples has been re-styled thanks to styler::style_pkg(), see dev/02_update.R for details.
SIGNIFICANT USER-VISIBLE CHANGES
- Switched from Travis to GitHub actions through usethis.
- Build the documentation website automatically with pkgdown.
- Added a dev/01_setup.R script.
- Now using a README.Rmd file.
SIGNIFICANT USER-VISIBLE CHANGES
- Use GenomeInfoDb::getChromInfoFromUCSC() when possible instead of data from biovizBase::hg19Ideogram for getting the hg19 chromosome lengths.
SIGNIFICANT USER-VISIBLE CHANGES
- Added a
NEWS.mdfile to track changes to the package.
NEW FEATURES
- Add ORCID's following changes at http://bioconductor.org/developers/package-guidelines/#description
SIGNIFICANT USER-VISIBLE CHANGES
- Use BiocManager
BUG FIXES
- Fixed an issue in
plotCluster()on how it was loading thehg19IdeogramCytoobject from thebiovizBasepackage.
BUG FIXES
- Fixed an issue with a call to
GenomicRanges::gaps()that affected how the introns were plotting inplotRegionCoverage()when the underlying data has a specifying start and end of the chromosome (that is, aseqinfo()withseqlengthsspecified). Thanks to Emily E Burke for reporting this issue https://github.com/emilyburke.
SIGNIFICANT USER-VISIBLE CHANGES
- Vignette now uses the new
BiocStyle::html_document()that was recently released.
SIGNIFICANT USER-VISIBLE CHANGES
- Help pages now document advanced arguments.
BUG FIXES
- Updated links to BrainSpan. Issue reported by Steve Semick https://github.com/SteveSemick.
SIGNIFICANT USER-VISIBLE CHANGES
- Dropped defunct functions.
BUG FIXES
plotRegionCoverage()used to take into account the strand of the regions for finding transcripts that overlapped the regions. This was not a problem with DERs from derfinder since they have strand*by default but it is a problem when using it with stranded regions.plotCluster()will also now ignore strand for finding neighboring regions.
SIGNIFICANT USER-VISIBLE CHANGES
- Only use distance if it's not
NAinplotRegionCoverage()
SIGNIFICANT USER-VISIBLE CHANGES
- Dropped
tMatrix()because it was a confusing plot and also lead to build errors.
NEW FEATURES
- Added the function
tMatrix()which uses aGRangesobject that has a variable of interest to compute t-Statistics between bins of the genome. For each bin, the values of the variable of interest from the regions overlapping the bin are used. We use t-Statistics instead of correlation because not all bins will have the same number of regions. This type of plot is similar to interaction plots made for HiC data.
NEW FEATURES
- Added the
vennRegions()function to visualize how many regions overlap known exons, introns, intergenic regions, none of them or several of these groups.
SIGNIFICANT USER-VISIBLE CHANGES
- Deprecated functions with underscores in their names in favor of camelCase functions. This was done to simplify the package.
SIGNIFICANT USER-VISIBLE CHANGES
- Adapted to work with
bumphunterversion >= 1.7.6
BUG FIXES
- Adapted
plotCluster()andplotOverview()to derfinder 1.1.5
NEW FEATURES
- Preparing to submit to Bioconductor.
- Added tests and vignette.
SIGNIFICANT USER-VISIBLE CHANGES
plotOverview()andplotCluster()can now plot FWER adjusted p-values if calculated withderfinder::mergeResults()
SIGNIFICANT USER-VISIBLE CHANGES
- Hid some arguments in
plotCluster()andplotOverview()as advanced just like inderfinderv0.0.74
BUG FIXES
- Improved the speed in
plotRegionCoverage()thentxdbis specified. Also fixed the introns on the gene track.
SIGNIFICANT USER-VISIBLE CHANGES
plotRegionCoverage()now has atxdbargument. When specified, this function will extract the transcript information needed and display the transcripts.
SIGNIFICANT USER-VISIBLE CHANGES
- Moved plotting functions from derfinder into this package