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().BUG FIXES
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.BUG FIXES
locate_url() for GTEx & TCGA BigWig files.NEW FEATURES
NEWS.md file to track changes to the package.