Release v0.6.4

• Adds a function (choose_tx) to select a subset of transcripts per junction that are more likely to be affected by a junction.
• Removal of the column "AS_event_ID" from the RNA junction output
• exon_in_intron() now expects a data.frame

Release v0.6.3

• parse_pangolin and format_pangolin support Pangolin decrease scores (negative scores)
• parse_pangolin is generalized to to Pangolin output generated with optional Pangolin parameter -s
• parse_pangolinworks for vcfs with only one variant
• spliceai_output.pangolin.vcf is updated
• annotate_mut_junc should remove predicted effects outside of transcript range
• add_peptide returns full protein sequence until first stop codon

Release v0.6.2

• ensure correct exon usage in MMSplice annotation (get_exon_skipping_junction / get_exon_inclusion_junction) by comparing genomic location of exons in MMSplice output and genomic location in database
• two functions to filter for unique junctions based on mut_id, junc_id and tx_id based on the highest effect score (unique_mut_junc() , unique_junc_mmsplice() )
• Readme now contains information how to optionally consider gene annotation in formatting of SpliceAI and Pangolin results
• combine_mut_junc() now merges based on mut_id, junc_id, tx_id again. It is recommended to apply the new uniqueness functions (unique_mut_junc() , unique_junc_mmsplice() ) before combining the data

Release v0.6.1

• annotate_mut_effect() now optionally considers transcripts restricted to genes directly provided by SpliceAI or Pangolin
• Column class was renamed to event_type
• combine_mut_junc() now returns rows that are unique based on mut_id, junc_id, tx_id, event_type
• updated README
• updated description of add_peptide()

Release v0.6.0

Major changes

• major update of add_peptide() function.
• annotate if junction leads to frame_shift
• revised format of resulting peptide sequence:
  • frame_shift: WT flanking size + until next stop codon
  • non frame_shifts: WT flanking size + novel sequence/breakpoint + WT flanking size/until next stop codon

Minor changes

• minor bug fix in exon_in_intron() function
• update to Roxygen-7.2.3
• more tests on add_peptide() function
• add column cds_description to better understand why peptide_context is NA in sanity checks. Can be one of c("mutated cds", "truncated cds", "no mutated gene product", "no wt cds", "not in ORF")

Release v0.5.6

• support stringr >= 1.5.0
• update CI with GitHub Actions

Release v0.5.5

• integrate splicing mutation tool Pangolin
• generalize mutation effect annotation

Release v0.5.4

• Update of Readme
• adds function exon_in_intron. This function determines if a predicted retained intron is covered by an an exon of another transcript or is exon-free

Release v0.5.3

This release:

*adapts splice2neo to easyquant 0.4.0. (https://github.com/TRON-Bioinformatics/easyquant)
*prevents annotate_spliceai function from failing in case of empty input
*adds some more tests

Release v0.5.2

The easyquant parsing functions were adjusted for the new interval mode.

Note: Easyquant has been changed meanwhile and the next splice2neo will provide compatibility