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.