2.5.4 (2024-01-31)
2.5.3 (2024-01-30)
- canonical transcript mapped read extraction (#77) (52b56b0)
- the above pull request also accumulated a number of other bug fixes and updates:
- QuantSeq data now also works with standard canonical transcripts, when MANE transcripts are not available for a species
- some environment and wrapper updates and fixes, e.g. biomart, pysam, sleuth, datavzrd
- some overall cleanup of the QuantSeq parts of the workflow
- proper QuantSeq testing data, generated with a dedicated workflow and hosted on Zenodo, which enables a quick and useful testing for the respective parts of the workflow
2.5.2 (2023-09-14)
- simpler three prime QuantSeq cutadapt setup (#78) (ecc9ab7)
- update samtools.yaml to latest
1.17
and update github actions (#75) (0fe7948)
2.5.1 (2023-06-14)
2.5.0 (2023-05-13)
2.4.3 (2023-02-06)
2.4.2 (2022-12-02)
- fix gene-level p-value adjustment (use Benjamini-Hochberg instead of Bonferroni-Holm) (#64) (6ea1682)
2.4.1 (2022-11-04)
- channel order for bioconductor package download (f57044a)
- correct default value for representative_transcripts and check for existence of path (#59) (a85b268)
- fix channel order under strict priorities (bdbfb10)
- fix default minimum p-value in fgsea (#61) (a6a857d)
- for some rules, omit software env when caching (#63) (1d2e3a9)
2.4.0 (2022-03-29)
- adapt to fgsea updates, configure fgsea precision by minimum achievable p-value (dcd77ca)