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