recountWorkflow 1.29.2

SIGNIFICANT USER-VISIBLE CHANGES

Implement a workaround to lawremi/rtracklayer#83 which currently is limiting the ability to remotely access BigWig files using rtracklayer::import(). This affects the functions recount::expressed_regions(), recount::coverage_matrix(), and derfinder::getRegionCoverage() used in recountWorkflow.

recountWorkflow 1.11.2

SIGNIFICANT USER-VISIBLE CHANGES

Documentation website is now available at http://LieberInstitute.github.io/recountWorkflow/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.
Added a NEWS.md file to track changes to the package.

recountWorkflow 1.11.2

BUG FIXES

Fix the spelling of RIN to rin now that all SRA columns are in lower case.
Fix the DESCRIPTION file (had a missing comma).

recountWorkflow 1.11.1

NEW FEATURES

Piggyback on GenomicState now that this package produces all the pieces needed for making the ER plots.
Potentially everything works on Windows now that rtracklayer::import.bw() seems to work there. But I haven't tested it.

BUG FIXES

Update SRARunTable.txt reading code since they changed the format on delivered by SRA. Adjust variables accordingly.

recountWorkflow 1.7.2

BUG FIXES

Fix the call to bumphunter::annotateTranscripts().
See https://gist.github.com/lcolladotor/196dabeb1ac628c35656bfa94b5d9577 for more details.

recountWorkflow 1.7.1

BUG FIXES

Fix the ftp url for the Gencode v25 gtf file.

recountWorkflow 1.3.1

SIGNIFICANT USER-VISIBLE CHANGES

Use BiocManager

recountWorkflow 0.99.0

NEW FEATURES

Created the workflow.