NEWS

---

recount3 1.21.1

BUG FIXES

• Switched from pryr to lobstr. This was done by @gpertea.

recount3 1.19.3

SIGNIFICANT USER-VISIBLE CHANGES

• We have verified that the data hosted by IDIES at JHU is accessible via either https://idies.jhu.edu/recount3/data or https://data.idies.jhu.edu/recount3/data/. See https://github.com/LieberInstitute/recount3/issues/58 for the details.

recount3 1.19.2

SIGNIFICANT USER-VISIBLE CHANGES

• recount3 no longer suggests using interactiveDisplayBase::display() as that package will be deprecated on bioc-devel. While the interactive sub-setting of a table was a nice little feature, it was not an important feature. Related to https://github.com/LieberInstitute/recount3/issues/57.

recount3 1.19.1

BUG FIXES

• Fixed a bug in file_retrieve() as noted at https://github.com/LieberInstitute/recount3/issues/56. The bug and solution to it was reported by @LiNk-NY.

recount3 1.11.2

SIGNIFICANT USER-VISIBLE CHANGES

• Windows users can now use http://duffel.rail.bio/recount3 again! The switch to httr::http_error() resolved the duffel access problem for Windows users.

recount3 1.11.1

SIGNIFICANT USER-VISIBLE CHANGES

• Switched from using RCurl::url.exists() to !httr::http_error().

recount3 1.3.9

BUG FIXES

• Resolved https://github.com/LieberInstitute/recount3/issues/7.

recount3 1.3.7

NEW FEATURES

• Added the create_hub() function for creating UCSC track hub configuration files for using the UCSC Genome Browser to explore the recount3 BigWig base-pair coverage files.

recount3 1.3.2

SIGNIFICANT USER-VISIBLE CHANGES

• rowRanges(rse_gene)$score is now rowRanges(rse_gene)$bp_length to make it easier to use recount::getTPM() and recount::getRPKM() with recount3 objects. Resolves https://github.com/LieberInstitute/recount3/issues/4.

BUG FIXES

• Updated read_metadata() based on https://github.com/LieberInstitute/recount3/issues/5. The empty metadata will be dropped with a warning in situations like that.

recount3 1.1.7

BUG FIXES

• read_counts() now reads the gene/exon counts for every sample as numeric instead of integer in order to support count values that exceed the 32bit integer threshold (such as 2447935369). Previously, read_counts() would report tiny fractions for such large numbers. This bug was reported by Christopher Wilks.

recount3 1.1.6

BUG FIXES

• Now project_homes() reads in a text file from recount3_url/organism/homes_index which enables support for custom URLs such as http://snaptron.cs.jhu.edu/data/temp/recount3test.

recount3 1.1.4

BUG FIXES

• Fixed project_homes(), available_projects() and available_samples() to support using non-standard recount3_urls where the user knows that are the project_homes() for their organism of choice. This fix enables users to create their own custom recount3-like webservers and access their data using the functions in this package. This fix introduces the argument available_homes to both available_projects() and available_samples(). This bug was reported by Christopher Wilks.

recount3 1.1.3

NEW FEATURES

• Added expand_sra_attributes() that was contributed by Andrew E Jaffe. This function expands the SRA attributes stored in a given SRA study, which makes it easier to use that data. However, it makes it harder to merge studies and thus should be used with caution.

recount3 1.1.1

BUG FIXES

• Fixed locate_url() for GTEx & TCGA BigWig files.

recount3 0.99.0

NEW FEATURES

• Added a NEWS.md file to track changes to the package.
• Documentation website is now available at http://LieberInstitute.github.io/recount3/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.