Changes in version 1.3.9                        

BUG FIXES

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

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 1.1.1                        

BUG FIXES

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

                       Changes in version 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.