NEWS
atena 1.10.0 (2024-04-27)
USER VISIBLE CHANGES
- Annotation metadata is now propagated to parameter and resulting SummarizedExperiment objects, which can be retrieved using 'mcols(features(x))' and 'mcols(rowRanges(x))' methods, respectively.
- The TE subclass annotation getter functions 'getLTRs()', 'getLINEs()', 'getSINEs()' and 'getDNAtransposons()' work now with both, parameter and resulting SummarizedExperiment objects.
- Manual pages and the vignette have been updated to illustrate the previous changes.
BUG FIXES
- Several bug fixes, mostly in how annotation metadata was stored and propagated.
atena 1.6.0 (2023-04-20)
USER VISIBLE CHANGES
- Improvement of the accuracy of the atena expression quantification method.
- Fixed numerical instability in TEtranscripts method.
- Added function (.matchSeqinfo) to harmonize seqinfo() of object with alignments and object with feature annotations.
- Implemented 'OneCodeToFindThemAll' annotation parser for RepeatMasker annotations.
- Implemented 'atena' annotation parser for RepeatMasker annotations.
- Added examples in the vignettes of TE annotation preprocessing steps using the implemented parsers.
- Changed default value of geneFeatures to NULL in the parameters objects.
- Improvement of the accuracy of the atena expression quantification method.
- Fixed numerical instability in TEtranscripts method.
- Added function (.matchSeqinfo) to harmonize seqinfo() of object with alignments and object with feature annotations.
- Implemented 'OneCodeToFindThemAll' annotation parser for RepeatMasker annotations.
- Implemented 'atena' annotation parser for RepeatMasker annotations.
- Added examples in the vignettes of TE annotation preprocessing steps using the implemented parsers.
- Changed default value of geneFeatures to NULL in the parameters objects.
BUG FIXES
- Fixed bug for not properly paired reads.
- Fixed bug for not properly paired reads.
atena 1.4.0 (2022-11-31)
USER VISIBLE CHANGES
- Implemented 'choose', 'average' and 'conf' reassignment modes in Telescope method.
- Creation of a 4th expression quantification method, called the atena method.
- Modified 'ovUnion' method to address alignments overlapping > 1 feature.
- Implemented 'OvIntersectionStrict' overlapping method.
- Adapted annotaTEs() function to new RepeatMasker annotations in AnnotationHub.
- Changed coercions to dgCMatrix and lgCMatrix to go via virtual classes to comply with latest updates in Matrix version 1.4-2.
atena 1.2.0 (2022-04-21)
USER VISIBLE CHANGES
- Higher accuracy in TE quantification for TEtranscripts and Telescope methods.
- Improved EM step running time.
- New AnnotationHub resource has been added: UCSCRepeatMasker.
- Implemented function to retrieve and parse TE annotations.
atena 0.99.36 (2021-08-01)
USER VISIBLE CHANGES
- Submission of the first version to the Bioconductor project.