DROP 1.6.1

What's changed in DROP 1.6.1

• fix bioconductor function deprecations by @c-mertes in #666
• bump drop version to 1.6.1 by @c-mertes in #667

Full Changelog: 1.6.0...1.6.1

DROP 1.6.0

DROP 1.6.0 release

The new release of DROP 1.6.0 includes the following changes:

• Fix MAE by removing unneeded seqlevel conversions by @vyepez88 in #661
• Enforce stringent boolean conversion from sample sheet by @c-mertes in #657
• DNA-RNA matching conf int. by @vyepez88 in #659
• Full test scripts based on Kremer et al data by @c-mertes in #663
• Use correct ID for MAE by @c-mertes in #664
• Release 1.6 by @c-mertes in #656

We thank also @AtaJadidAhari for his contributions

Full Changelog: 1.5.0...1.6.0

DROP 1.5.0

• Contains the versions of OUTRIDER and FRASER that use the Optimal Hard Threshold procedure. This leads to a reduction in the run time of around 6-10 times (#615)
• DROP now supports mixing BAM files and external expression counts within the same group (#631)
• Other updates from FRASER:
  • Fixes a bug in split-reads counting in cohorts of single-end data
  • Fixes a bug in assigning gene names to junctions
• Reduces run-time of DNA-RNA matching (#644)
• Fixes a bug in sex-matching algorithm
• Multithreading expression counting per chromosome and run MAE counting in parallel per chromosome (#633)

DROP 1.4.0

• FRASER counting is done using the strand of each sample instead of the strand of the whole cohort
• FRASER results no longer contain sample annotation info
• If a subset of genes to test were provided, the FRASER results are now tidy -> one row per event with multiple columns containing all the p-values and adjusted p-values
• Sample annotation file now must always contain STRAND for all samples, including external ones

DROP 1.3.4

• fixes the FRASER version to 1.99.3 commit d6a422c to ensure reproducibility
• fixes the OUTRIDER version to 1.20.1
• fixes certain scripts affected by a snakemake update

DROP 1.3.3

Fixes a bug when compiling the aberrant splicing results.

DROP 1.3.2

Fixes issues with having only 1 internal sample. Simplifies the counting Summary html in the aberrant splicing module.

DROP 1.3.1

• small bugfix in the Aberrant Splicing Counting Summary Script when providing only 1 external sample

DROP 1.3.0

• Supports FRASER 2.0, an improved version that uses the Intron Jaccard Index as its single splice metric
• Allows to provide lists of genes to test during FDR correction in addition to the transcriptome-wide FDR across all expressed genes

DROP 1.2.4

What's Changed

• Bug Fixes in MAE
• yieldSize and dnaRnaMatchCutoff config values
  • yieldSize: allows for memory consideration in VCF and BAM file processing
  • dnaRnaMatchCutoff: sets the threshold for MAE sample matching
• Summary edits to aberrantSplicing

Full Changelog: 1.2.3...1.2.4