FRASER - FRASER 2.4.5

Fixes a bug with the split read counting. It matters for unstranded, paired-end data.

- R
Published by vyepez88 6 months ago

FRASER - FRASER 2.4.5

Fixes a bug with the split read counting. It matters for unstranded, paired-end data.

- R
Published by vyepez88 6 months ago

FRASER - FRASER 2.4.3

Fixes a bug with the cache

- R
Published by vyepez88 9 months ago

FRASER - FRASER 2.4.2

• We are now releasing FRASER 2.4.2 an improved algorithm with respect to FRASER that uses the Intron Jaccard index. This also makes it 2-3 times faster and lighter!
• In addition, instead of doing a grid search to determine the optimal encoding dimension of the denoising autoencoder, we now use the Optimal Hard Threshold (OHT). This makes the algorithm 6-10 times faster!
• Note that since this version, FRASER is not for commercial use

- R
Published by vyepez88 9 months ago

FRASER - bioRxiv submission

Version used to create all results in the bioRxiv paper

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

- R
Published by c-mertes over 1 year ago

FRASER - FRASER 1.99.3

• Vignette updates by @ischeller in https://github.com/c-mertes/FRASER/pull/58
• Fix tests by @ischeller in https://github.com/c-mertes/FRASER/pull/68
• update BIOC version by @AtaJadidAhari in https://github.com/c-mertes/FRASER/pull/69
• fix GHA cache address by @AtaJadidAhari in https://github.com/c-mertes/FRASER/pull/71

Full Changelog: https://github.com/c-mertes/FRASER/compare/1.99.2...1.99.3

- R
Published by c-mertes over 1 year ago

FRASER - 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

- R
Published by c-mertes almost 2 years ago

FRASER - FRASER 1.99.3

• bug fix to avoid error for contig names containing certain characters

- R
Published by ischeller almost 3 years ago

FRASER - FRASER 1.99.2

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

- R
Published by ischeller almost 3 years ago

FRASER - 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

- R
Published by ischeller almost 3 years ago

FRASER - FRASER 1.8.1

Bugfix in merging splicing counts (#41)

- R
Published by c-mertes over 3 years ago

FRASER - 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)

- R
Published by c-mertes almost 4 years ago

FRASER - FRASER 1.2.1

Add merging of external counts

- R
Published by c-mertes about 5 years ago

FRASER - FRASER 1.2.0

Major improvements and bugfixes. * Move from psiSite to theta * Use S4/S3 methods together with OUTRIDER

- R
Published by c-mertes over 5 years ago

FRASER - FRASER 1.1.3

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

- R
Published by c-mertes over 5 years ago