v2.5.2

2.5.2 (2023-09-14)

Bug Fixes

• simpler three prime QuantSeq cutadapt setup (#78) (ecc9ab7)
• update samtools.yaml to latest 1.17 and update github actions (#75) (0fe7948)

Performance Improvements

• bump datavzrd wrapper to 2.6.0 and general bug fixes (#80) (657c465)

v2.5.1

2.5.1 (2023-06-14)

Bug Fixes

• Updated the get-transcript-info.R file and its dependencies (#73) (e44d424)

v2.5.0

2.5.0 (2023-05-13)

Features

• Support for 3-prime RNA sequencing (#62) (c06c573)

Bug Fixes

• fix report labels (#72) (76c7fd9)

v2.4.3

2.4.3 (2023-02-06)

Bug Fixes

• Feature/update cutadapt wrapper (#67) (29d7967)

v2.4.2

2.4.2 (2022-12-02)

Bug Fixes

• fix gene-level p-value adjustment (use Benjamini-Hochberg instead of Bonferroni-Holm) (#64) (6ea1682)

v2.4.1

2.4.1 (2022-11-04)

Bug Fixes

• 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)

v2.4.0

2.4.0 (2022-03-29)

Features

• adapt to fgsea updates, configure fgsea precision by minimum achievable p-value (dcd77ca)

Version 2.3.2

• Fix a bug in sleuth_init that had previously led to a crash if ensembl metadata did not contain information about canonical transcripts.

Version 2.3.1

• A bug leading to a crash with custom representative transcript handling has been fixed.
• Differential splicing analysis can now be deactivated in the config.
• Various little usability bug fixes.

Version 2.3.0

• Extensive differential splicing analysis using IsoformSwitchAnalyzeR.
• Added ability to choose the strategy for which transcript to choose for gene based analysis (canonical from ensembl, most significant, custom ID list).
• Differential expression tables now also show the per sample normalized transcript expression.
• Expression matrix output is now batch effect corrected and based on log counts.
• Migration to R 4.1.
• Various little fixes for corner cases.