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GenomicMedLab
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cool-seq-tool
https://coolseqtool.readthedocs.io
MIT License
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chore: remove unused action
#376
jsstevenson
closed
4 days ago
0
fix!: Expect user to supply valid, case-sensitive HGNC symbol
#375
jarbesfeld
closed
5 days ago
2
Expect gene symbol to be formatted correctly
#374
jarbesfeld
closed
5 days ago
3
Ensure proper gene symbol comparison
#373
jarbesfeld
closed
3 weeks ago
0
Add warning for when a coordinate occurs outside of 100 base pairs of the start/end of a transcript
#372
katiestahl
opened
1 month ago
0
Add parameter for using GRCh37 sequences
#371
jarbesfeld
opened
1 month ago
1
fix: make gene optional param for converting genomic coords as long a…
#370
katiestahl
closed
1 month ago
0
Do not require gene when genomic accession and transcript are provided to genomic_to_tx_segment
#369
jarbesfeld
closed
1 month ago
0
Gene should be an optional parameter for genomic_to_tx_segment when transcript and genomic accession are provided
#368
jarbesfeld
closed
1 month ago
0
MANE transcript data was not found for the gene C1orf159
#367
jarbesfeld
closed
3 weeks ago
17
Ensure that start position does not exceed end position for a transcript segment
#366
jarbesfeld
opened
1 month ago
0
refactor: remove duplicate `genomic_ac` check
#365
korikuzma
closed
2 months ago
0
test: update tests for `ExonGenomicCoordsMapper`
#364
korikuzma
closed
1 month ago
6
Migrate staging changes to main branch
#363
korikuzma
closed
2 months ago
0
Break up `_genomic_to_tx_segment` into smaller methods
#362
korikuzma
opened
2 months ago
0
Choosing the Correct Adjacent Exon along Exon Boundaries
#361
jarbesfeld
opened
2 months ago
3
refactor: rename `_get_alt_ac_start_and_end` + flatten output
#360
korikuzma
closed
2 months ago
0
refactor: rename `is_start` kwarg in private methods to `is_seg_start`
#359
korikuzma
closed
2 months ago
1
refactor: reorder classes and methods in `exon_genomic_coords` module
#358
korikuzma
closed
2 months ago
0
refactor!: rename `ExonCoord` to `_ExonCoord` to indicate internal use
#357
korikuzma
closed
2 months ago
2
fix: genomic accession mismatch when getting nearest tx junction
#356
korikuzma
closed
2 months ago
1
docs: link to stable, not latest
#355
jsstevenson
closed
2 months ago
0
Update fixtures and offsets for test_exon_genomic_coords
#354
jarbesfeld
closed
2 months ago
0
feat: enable direct import of CST from package root
#353
jsstevenson
closed
2 months ago
0
feat!: update `ExonGenomicCoordsMapper` + `UtaDatabase`
#352
korikuzma
closed
2 months ago
2
feat!: return Pydantic model in `UtaDatabase.get_tx_exon_aln_v_data`
#351
korikuzma
closed
2 months ago
0
feat!: return Pydantic model in `get_alt_ac_start_or_end`
#350
korikuzma
closed
2 months ago
1
refactor: remove unnecessary literal from `AnnotationLayer` enum
#349
korikuzma
closed
2 months ago
0
feat!: remove `UtaDatabase.get_tx_exons_genomic_coords`
#348
korikuzma
closed
2 months ago
0
feat!: remove `UtaDatabase.get_tx_exons` + cleanup exon work
#347
korikuzma
closed
2 months ago
0
[OLD] feat!: update `ExonGenomicCoordsMapper`
#346
korikuzma
closed
2 months ago
3
Wrong location in `ExonGenomicCoordsMapper.transcript_to_genomic_coordinates`
#345
jsstevenson
closed
2 months ago
3
feat!: remove optional `coordinate_type` from `genomic_to_tx_segment`
#344
korikuzma
closed
2 months ago
2
feat!: rename `start`/`end` to `genomic_start`/`genomic_end` in `genomic_to_tx_segment`
#343
korikuzma
closed
2 months ago
1
Add information about Ensembl transcripts to docs
#342
korikuzma
opened
3 months ago
0
Add coordinate type to usage docs
#341
korikuzma
opened
3 months ago
0
refactor: remove optional `strand` field from `genomic_to_tx_segment`
#340
korikuzma
closed
2 months ago
1
feat!: move `get_tx_exons_genomic_coords` to `ExonGenomicCoordsMapper`
#339
korikuzma
closed
2 months ago
2
feat!: rename ExonGenomicCoordsMapper methods
#338
korikuzma
closed
3 months ago
0
feat!: rename residue mode to coordinate type
#337
korikuzma
closed
3 months ago
0
Move pydantic models to their respective module
#336
korikuzma
opened
3 months ago
0
Rename residue mode to coordinate type
#335
korikuzma
closed
3 months ago
3
feat!: Return Pydantic models instead of dicts in UtaDatabase
#334
korikuzma
closed
3 months ago
0
docs: remove VRS schema support section
#333
korikuzma
closed
3 months ago
0
Counterintuitive/wrong? offset from genomic to transcript mapping
#332
jsstevenson
closed
2 months ago
3
docs: fix source link
#331
jsstevenson
closed
3 months ago
0
Add start/end residue mode parameter
#330
korikuzma
closed
3 months ago
2
"Start chr does not match end chr" when calling `genomic_to_exon_coords` with one position in intronic space
#329
jsstevenson
closed
2 months ago
6
fix(test): remove fixture decorator from get_prioritized_transcripts_from_gene
#328
korikuzma
closed
3 months ago
0
`GenomicData` should include start/end for both start_exon and end_exon
#327
korikuzma
closed
3 months ago
24
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