CHANGES IN VERSION 1.6.0 (2023-04-20) ------------------------------------- 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) --------------------------------------- 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) --------------------------------------- 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) --------------------------------------- USER VISIBLE CHANGES o Submission of the first version to the Bioconductor project.