- add vignette with example workflow
- fix parsing of pangolin results
- simplify README
- Fixed bug while parsing VCF files containing only a single variant
- Improved error handling of spladder import
- add new function to select more relevant junction-transcript combinations
- adapt input and output of exon_in_intron()
- 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
- 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
- annotate_mut_effect() now optionally considers only transcripts from genes provided by SpliceAI or Pangolin
- Column
class
was renamed toevent_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()
- major update of add_peptide() function + adding some tests
- minor bug fix in exon_in_intron() function
- minor changes to support stringr >= 1.5.0
- integrate splicing mutation tool Pangolin
- generalize mutation effect annotation
- adds a function to annotate if a exon of another transcript is located in an intron
- update README
- 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
- support updated version of EasyQuant
- 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()
- intron rentetion 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 thects_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
- 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
- Leafcutterr: 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.
- minor update of doc and README
- 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
- 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
- This minor release adds a pseudo example to the README + simplifies the
transform_for_requant
function
- CI config for github action
- R CMD check
- test coverage with Codecov
- pkgdown website on github.io
- update README
- clean up code and doc
- 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
- inclusion of functions from previous repositories
- Added basic package structure
- Added functions
parse_spliceai()
andformat_spliceai()
- Automatic build of pkgdown website