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