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NEWS.md

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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

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