CHANGES IN VERSION 0.99.2 (2020-04-22)
-------------------------------------

NEW FEATURES

    o First submission of metaseqR2

CHANGES IN VERSION 1.1.13 (2020-05-25)
-------------------------------------

NEW FEATURES

    o Addition of the harmonic mean p-value combination method
    (Wilson, 2019 - https://doi.org/10.1073/pnas.1814092116)
    o Addition of a new dataset (hg19pvalues) containing a set of
    gene p-values from Giakountis et al., 
    https://doi.org/10.1016/j.celrep.2016.05.038 to be used in the
    main vignette as well as a playground for p-value combination
    
BUG FIXES

    o Major bug fix! The order of p-values returned by statDss was
    inconsistent with the rest of the stat* functions.
    o Other minor bug fixes.

CHANGES IN VERSION 1.1.15 (2020-06-12)
-------------------------------------

NEW FEATURES

    o Allow simple differential exon analysis
    
BUG FIXES

    o Fixed annotation breaks from UCSC (rn, danRer).
    o Fixed crash when using excludeList (due to attributes being gone after
    list subsetting).

CHANGES IN VERSION 1.1.16 (2020-06-22)
-------------------------------------

NEW FEATURES

    o Added support for reading targets in YAML
    
BUG FIXES

    o Fixed "rnacomp" plot trying to import to JSON db while not run.
    o Fixed report crash when "exportWhere" was NA.
    o Other minor bug fixes

CHANGES IN VERSION 1.1.17 (2020-06-29)
-------------------------------------

NEW FEATURES

    o Integrated functionalities from deprecated packages DESeq and
    NOISeq in order to maintain PANDORA
    
BUG FIXES

    o Fixed report crash with the new readTargets wrapper function.

CHANGES IN VERSION 1.1.18 (2020-07-03)
-------------------------------------

NEW FEATURES

    o Simple quantification, QC and reporting is now allowed without having
    to define a contrast or statistical tests to be performed. 
    o In case of only a contrast is defined but no statistical tests required
    only fold changes are calculated.
    
BUG FIXES

    o Fixed undefined class/function leftovers from NOISeq integration.

CHANGES IN VERSION 1.1.19 (2020-07-29)
-------------------------------------

NEW FEATURES

    o None
    
BUG FIXES

    o Fixed several problems with respect to custom GTF annotation import,
    especially when the GTF is compliant with minor GTF standards.
    o Fixed a few warnings resulting in errors in R>4.0.

CHANGES IN VERSION 1.1.21 (2020-08-05)
-------------------------------------

NEW FEATURES

    o Creation of UCSC track and assembly hubs through the provision of a FASTA
    genome and/or assembly file for a non-supported or custom organism.
    
BUG FIXES

    o Fixed a problem with rownames when importing an existing counts table.

CHANGES IN VERSION 1.3.13 (2021-02-20)
-------------------------------------

NEW FEATURES

    o Ability to use a different sample list with different condition names but
    same sample set (or subset) with a previous gene model with same samples.
    
BUG FIXES

    o None.

CHANGES IN VERSION 1.5.1 (2021-06-14)
-------------------------------------

NEW FEATURES

    o None.

BUG FIXES

    o Fix in annotation backwards compatibility.
    o Fix bigGenePred gene annotation track generation.


CHANGES IN VERSION 1.13.2 (2023-10-04)
-------------------------------------

NEW FEATURES

    o None.

BUG FIXES

    o Removed the deprecated baySeq from PANDORA

CHANGES IN VERSION 1.15.1 (2024-03-07)
-------------------------------------

NEW FEATURES

    o None.

BUG FIXES

    o Fixed supported Ensembl annotation versions
