bioRxiv submission

Version used to create all results in the bioRxiv paper

This tag was created for completeness, but should not be used anymore.

FRASER 1.99.4

• Fixed drop parameter in generic [ function and other small bug fixes #62
• Implemented sample specific counting regarding strandSpecific parameter #72 and #76
• Fix error when intron not on same chr as any genes in the txdb #75
• Small updates in the documentation #58

FRASER 1.99.3

• Vignette updates by @ischeller in #58
• Fix tests by @ischeller in #68
• update BIOC version by @AtaJadidAhari in #69
• fix GHA cache address by @AtaJadidAhari in #71

Full Changelog: 1.99.2...1.99.3

FRASER 1.99.2

• update plot functions to color aberrant status based on pvalues computed on subsets of genes

FRASER 1.99.0

• Move to FRASER 2.0, using the Intron Jaccard Index as its single splice metric
• Supports restriction of FDR correction to specific genes based on prior knowledge
• Several small improvements

FRASER 1.8.1

Bugfix in merging splicing counts (#41)

FRASER 1.6.1

• Fixing quantile filtering defaults (#28)
  • Require min expression in 5% instead of 95% of the samples
  • Require min expression on both sides of the junction
• Align FRASER package with DROP pipeline (#24)
• Move temp directory from tempdir() to working directory getwd() (#35)
• Improve visualizations and Improve documentation
• Improve internal object validation
• Minor bugfixes (eg. #37)

FRASER 1.2.1

Add merging of external counts

FRASER 1.2.0

Major improvements and bugfixes.

• Move from psiSite to theta
• Use S4/S3 methods together with OUTRIDER

FRASER 1.1.3

The 1.1.3 version is used to run the full pipeline in our accompanying paper