NEWS.md

In acidgenomics/freerange: Generate and Manipulate Genomic Ranges

freerange 0.2.8 (2019-11-06)

Minor changes

• Updated dependencies to require Bioconductor 3.10 release.

freerange 0.2.7 (2019-10-22)

Minor changes

• NAMESPACE updates reflecting migration of some low-level functions into new acidbase package.

freerange 0.2.6 (2019-09-25)

Minor changes

• Tweaked internal code to only call camelCase on character vectors, instead of attempting to directly sanitize GRanges or DataFrame class objects. The Bioconductor S4 methods capable of these approaches have been moved from syntactic to basejump.

freerange 0.2.5 (2019-09-06)

Minor changes

• makeGRangesFromGFF: Added ignoreTxVersion argument, similar to tximport convention, which allows the user to rename the transcriptID column to include the transcript version (e.g. ENST00000000233.10). This is useful for matching identifiers in kallisto output processed directly from an Ensembl FASTA reference transcriptome.
• Updated unit tests to check against Ensembl 97, from Ensembl 87.

freerange 0.2.4 (2019-08-27)

Updated R dependency to 3.6.

freerange 0.2.3 (2019-08-21)

Major changes

• makeGRangesFromEnsembl: Bug fix for recent ensembldb update that added AH73986 (Ensembl 79), which appears to be newer than AH73881 (Ensembl 97) when sorting by AnnotationHub identifier. We've hardened the internal code to instead sort by title, which resolves this issue.

freerange 0.2.2 (2019-08-14)

Minor changes

• Improved message consistency.
• Updated dependency verisons.

freerange 0.2.1 (2019-08-05)

Minor changes

• Improved documentation consistency using new acidroxygen package.

freerange 0.2.0 (2019-07-22)

Bumped version to reflect change in basejump dependencies.

freerange 0.1.9 (2019-07-16)

Minor changes

• Updated basejump dependencies.
• Improved code coverage.
• Updated Travis CI Docker configuration.

freerange 0.1.8 (2019-06-07)

Minor changes

• Migrated Ensembl release to host matching code involving biomaRt to basejump.

freerange 0.1.7 (2019-06-06)

New data

• Added ensemblReleaseArchive data, which maps the Ensembl release to the Ensembl archive host URL.

freerange 0.1.6 (2019-05-06)

Major changes

• Now pinned to R >= 3.5.

Minor changes

• Updated basejump dependencies, reflecting change in brio package.

freerange 0.1.5 (2019-05-02)

Minor changes

• makeGRangesFromEnsembl: Detect organisms with complex names including 3 words (e.g. Canis lupus familiaris) and automatically sanitize to the 2 word convention used internally by ensembldb (e.g. Canis familiaris). Thanks @umasaxena for the heads up on this.

freerange 0.1.4 (2019-04-25)

Minor changes

• S4 generic reexport documentation fixes.

freerange 0.1.3 (2019-04-22)

Minor changes

• Backward compatibility fixes/updates for BioC 3.6 / R 3.4.

freerange 0.1.2 (2019-04-07)

Major changes

• emptyRanges: Renamed mcolsNames to mcolnames, for better consistency with the basejump naming conventions. Note that this formal is currently used by basejump and bcbioSingleCell.

Minor changes

• Reworked unit tests to improve code coverage above 90%.
• Added back data-raw/ scripts used to general minimal GFF example files.
• .makeGenesFromEnsemblGTF and .makeTranscriptsFromEnsemblGTF: Made assert checks less strict. No longer requiring gene_biotype or gene_name, so we can pass through GRanges generated from FlyBase or WormBase.

Future considerations

• Still not removing gene and transcript version numbers for GENCODE GFF files. Consider changing this convention in a future update.

freerange 0.1.1 (2019-03-28)

Minor changes

• Renamed organism_mappings data to organismMappings, to improve camel case consistency in package.

freerange 0.1.0 (2019-03-27)

Initial release. Migrated Ensembl AnnotationHub and GFF/GTF parsing functions here from the basejump package.

acidgenomics/freerange documentation built on Jan. 8, 2020, 3:45 a.m.