NEWS

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metaseqR2 1.15.1 (2024-03-07)

NEW FEATURES

• None.

BUG FIXES

• Fixed supported Ensembl annotation versions

metaseqR2 1.13.2 (2023-10-04)

NEW FEATURES

• None.

BUG FIXES

• Removed the deprecated baySeq from PANDORA

metaseqR2 1.5.1 (2021-06-14)

NEW FEATURES

• None.

BUG FIXES

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

metaseqR2 1.3.13 (2021-02-20)

NEW FEATURES

• 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

• None.

metaseqR2 1.1.21 (2020-08-05)

NEW FEATURES

• 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

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

metaseqR2 1.1.19 (2020-07-29)

NEW FEATURES

• None

BUG FIXES

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

metaseqR2 1.1.18 (2020-07-03)

NEW FEATURES

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

BUG FIXES

• Fixed undefined class/function leftovers from NOISeq integration.

metaseqR2 1.1.17 (2020-06-29)

NEW FEATURES

• Integrated functionalities from deprecated packages DESeq and NOISeq in order to maintain PANDORA

BUG FIXES

• Fixed report crash with the new readTargets wrapper function.

metaseqR2 1.1.16 (2020-06-22)

NEW FEATURES

• Added support for reading targets in YAML

BUG FIXES

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

metaseqR2 1.1.15 (2020-06-12)

NEW FEATURES

• Allow simple differential exon analysis

BUG FIXES

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

metaseqR2 1.1.13 (2020-05-25)

NEW FEATURES

• Addition of the harmonic mean p-value combination method (Wilson, 2019 - https://doi.org/10.1073/pnas.1814092116)
• 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

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

metaseqR2 0.99.2 (2020-04-22)

NEW FEATURES

• First submission of metaseqR2