Changelog

Source: NEWS.md

recountWorkflow 1.29.2

SIGNIFICANT USER-VISIBLE CHANGES

• Implement a workaround to https://github.com/lawremi/rtracklayer/issues/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.