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.
