Changelog

Source: NEWS.md

splice2neo 0.6.14

• fix changed dependency package for makeTxDbFromGFF() function
• Require R >= 4.4
• add automated docker building support

splice2neo 0.6.13

• Fixed bug leading to incorret peptide sequences
• Simplified code of add_peptide() function
• Added function to calculate distances to next canonical splice sites
• Added function to annotate if junction is potentially a JET (Exon-TE chimera)

splice2neo 0.6.12

• Add docker container support
• support parsing of junctions with no strand info from STAR output

splice2neo 0.6.11

• fix of liftover function
• improve warning and add more tests
• update of combine_mut_junc() to accept empty tables as input
• update of format_cispliceai() to optionally keep gene_ids
• add more test

splice2neo 0.6.9

• Simplification of function annotate_mut_effect() and ensuring that return of same column names in case of empty output

splice2neo 0.6.8

• Add function `liftover_junc_id() to liftOver splice junctions to other reference genomes or personalized genomes

splice2neo 0.6.7

Added:

• Functionality from splice2neo_neoants:
  • CI-SpliceAI parsing and formatting functions with example data and tests
  • IRFinder parsing and filtering functions with example data and tests
  • StringTie parsing and formatting functions
  • SUPPA2 parsing and formatting functions
  • STAR parsing and formatting functions with example data and tests
  • RegTools parsing and formatting functions with example data and tests
• add test for empty CI-SpliceAI input file
• add more global variables to avoid notes in R CMD check

Changed:

• Update CI/CD pipeline for less verbosity during R pkg installations
• Return single-row data.frame for empty input in annotate_mut_effect()
• include ’number_of_supporting_reads` when parsing SplAdder output
• generalize generate_combined_dataset() to multiple inputs
• Update README with list of supported tools
• add option consider_intron_retention to annotate_mut_effect()
• adjust syntax for dplyr >= 1.1.1
• remove rarely used pkgs from Imports
• simplify code in parse_spliceai_thresh()
• minor spell check fixes and doc updates

Fixed:

• fix warnings due to NA’s in CI-SpliceAI parsing function
• fix use of generate_combined_dataset() in vignette

splice2neo 0.6.6

• add vignette with example workflow
• fix parsing of pangolin results
• simplify README

splice2neo 0.6.5

• Fixed bug while parsing VCF files containing only a single variant
• Improved error handling of spladder import

splice2neo 0.6.4

• add new function to select more relevant junction-transcript combinations
• adapt input and output of exon_in_intron()

splice2neo 0.6.3

• revision of parse_pangolin and format_pangolin functions
• annotate_mut_junc should remove predicted effects outside of transcript range
• add_peptide returns full protein sequence until first stop codon

splice2neo 0.6.2

• ensure correct exon usage in MMSplice annotation
• two new functions to filter for unique junctions based on mut_id, junc_id and tx_id based on the highest effect score

splice2neo 0.6.1

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

splice2neo 0.6.0

• major update of add_peptide() function + adding some tests
• minor bug fix in exon_in_intron() function

splice2neo 0.5.6

• minor changes to support stringr >= 1.5.0

splice2neo 0.5.5

• integrate splicing mutation tool Pangolin
• generalize mutation effect annotation

splice2neo 0.5.4

• adds a function to annotate if a exon of another transcript is located in an intron
• update README

splice2neo 0.5.3

• 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

splice2neo 0.5.2

• support updated version of EasyQuant

splice2neo 0.5.1

• update annotate_spliceai_junction() to ignore donor loss and acceptor loss when not overlapping with wild-type junctions + IR must be within transcript range
• fix minor bugs in add_context_seq() and get_junc_pos()

splice2neo 0.5.0

• intron retention events are now supported by add_context_seq(). the resulting context sequence covers the complete intron instead of the exon/intron boundary only. Instead of a the junction position in the cts_seq, the positions are given in form of an interval in the cts_junc_pos column for intron retentions. (0,start_IR, end_IR, end_cts)
• add_peptide() was adjusted for intron retentions
• more tests were added for several functions
• fix small bug in annotate_spliceai_junction() that led to annotation with same transcript

splice2neo 0.4.1

• Support donor gain and acceptor gain in introns
• export annotate_spliceai_junction and canonical_junctions()
• More stable checks for correct format in generate_junction_id()
• Additional unit tests

splice2neo 0.4.0

• Leafcutter: The strand information while leafcutter parsing is now retrieved from the cluster id in the count table.
• Spladder: previous code changes missed to consider the event type in generation of the junc id for alternative splice sites. This is fixed now.
• More tests were added
• An old bug in spladder_transform_mutex_exon was fixed
• Until now a junc_id could appear multiple times if it could be part of multiple events. As we are not interested in re-constructing the events, now unique junc_ids will be returned.

splice2neo 0.3.1

• minor update of doc and README

splice2neo 0.3.0

• update of the junction id format: chr:start-end:strand
• new function:
  • generate_junction_id()
  • junc2breakpoint()
  • breakpoint2junc()
• The recent versions of leafcutter (v0.2.9) and spladder (v3.0.2) will be supported from now on.
• update and add unit tests
• update documentation and README
• visualization of modified junctions added

splice2neo 0.2.0

• new function:
  • bed_to_junc()
  • is_canonical()
  • is_in_rnaseq()
  • parse_gtf()
• updated functions:
  • add_context_seq()
  • add_peptide()
  • add_peptide()
  • get_junc_pos()
• faster implementation of modify_tx()
• update documentation and README
• update and add unit tests

splice2neo 0.1.3

• This minor release adds a pseudo example to the README + simplifies the transform_for_requant function

splice2neo 0.1.2

• CI config for github action
  • R CMD check
  • test coverage with Codecov
  • pkgdown website on github.io
• update README

splice2neo 0.1.1

• clean up code and doc

splice2neo 0.1.0

• New implementation of transcript modifications by junction
• New user interface functions that mainly work with data.frames:
  • add_tx()
  • modify_tx()
  • add_context_seq()
  • add_peptide()
• Updated toy example data sets
• First example in README

splice2neo 0.0.2

• inclusion of functions from previous repositories

splice2neo 0.0.1

• Added basic package structure
• Added functions parse_spliceai() and format_spliceai()
• Automatic build of pkgdown website