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