NEWS.md
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.BUG FIXES
file_retrieve() as noted at https://github.com/LieberInstitute/recount3/issues/56. The bug and solution to it was reported by @LiNk-NY.SIGNIFICANT USER-VISIBLE CHANGES
httr::http_error() resolved the duffel access problem for Windows users.SIGNIFICANT USER-VISIBLE CHANGES
RCurl::url.exists() to !httr::http_error().NEW FEATURES
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.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
read_metadata() based on https://github.com/LieberInstitute/recount3/issues/5. The empty metadata will be dropped with a warning in situations like that.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.BUG FIXES
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.BUG FIXES
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.NEW FEATURES
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.NEW FEATURES
NEWS.md file to track changes to the package.