: issues with the underlying SpliceAI model.
- updated to gencode v44 "basic" annotations (instead of comprehensive). These have fewer transcripts per gene.
- added demo of igv.js visualizations. TODO: allow users to select which tracks to show.
May 22, 2023
- changed defaults to 'masked' and max distance to 500bp
- retired
Illumina precomputed scores since they were created using Gencode v24
and max distance = 50bp and so can differ from computed scores which are based on the latest Gencode.
May 12, 2023
- added REF & ALT score columns to show SpliceAI's underlying predictions for each haplotype
(using
SpliceAI PR by @h-joshi).
The Δ score column is the difference between these two scores.
- added support for MNPs (see
issue #1 &
SpliceAI PR by @kdahlo)
- updated to
Gencode v43 (was previously on v42)
May 10, 2023
- fixed bug where "raw" Pangolin scores were shown regardless of whether the user selected "raw" or "masked".
Feb 5, 2023
- show
Pangolin scores in addition to SpliceAI scores.
June 2, 2021
- show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or more matching
RefSeq NM ids according to Ensembl. See
issue #8 for details.
April 11, 2021
- show gray background for non-coding transcripts
- switch to showing all non-coding transcripts. (Previously, transcripts with Gencode biotypes
like
lncRNA,
processed_pseudogene,
processed_transcript,
retained_intron, and
nonsense_mediated_decay were filtered out if they overlapped
protein_coding transcripts).
See
issue #6 for details.