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 #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 #4.

recount3 1.3.2

BUG FIXES

Updated read_metadata() based on #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.