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Sage-Bionetworks
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Genie
Validation and processing of GENIE files
https://genie.synapse.org/
MIT License
12
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[GEN-45] Add fusion caselist file
#478
thomasyu888
closed
2 years ago
0
Do sample comparison in memory due to limits
#477
thomasyu888
closed
2 years ago
0
Make sure to remove # when reading in data
#476
thomasyu888
closed
2 years ago
0
Improve maf processing
#475
thomasyu888
closed
2 years ago
0
Patch - Upper case the column headers for clinical file
#474
thomasyu888
closed
2 years ago
0
Release 14
#473
thomasyu888
closed
2 years ago
1
[IBCDPE-220] fix lgtm.com code scanning warnings/recommendations
#472
thomasyu888
closed
2 years ago
3
[IBCDPE-219] Create codeql.yml action
#471
thomasyu888
closed
2 years ago
2
[IBCDPE-218] add setupcfg
#470
thomasyu888
closed
2 years ago
0
[IBCDPE-215] Lint tests
#469
thomasyu888
closed
2 years ago
0
V13.3.0 rc
#468
thomasyu888
closed
2 years ago
0
updated required pandas version to be >=1.3.5
#467
thomasyu888
closed
1 year ago
0
Check CONTACT <= death dates
#466
thomasyu888
closed
1 year ago
0
Update SEQ_DATE error message
#465
thomasyu888
closed
1 year ago
0
allow for unknown interval but known year
#464
hhunterzinck
closed
2 years ago
0
Modify vital status inconsistency check
#463
hhunterzinck
closed
2 years ago
0
Rc 13.2.0
#462
thomasyu888
closed
2 years ago
0
[ETL-156] Use genie config in validation cli
#461
thomasyu888
closed
2 years ago
2
[ETL-159] Use GENIE config dict for processing
#460
thomasyu888
closed
2 years ago
2
[IBCSPRT-35] Add clinicalReported column to genomic information file
#459
thomasyu888
closed
2 years ago
0
Add clinicalReported to genomic information file
#458
thomasyu888
closed
2 years ago
0
assay information was being incorrectly processed
#457
thomasyu888
closed
2 years ago
0
Rc 13.1.0
#456
thomasyu888
closed
2 years ago
0
[ETL-156, ETL-157, ETL-158] Create configuration dictionary for GENIE code
#455
thomasyu888
closed
2 years ago
1
[IBCDPE-178] Create ValidationResult class
#454
thomasyu888
closed
2 years ago
0
support scheduled job secrets
#453
thomasyu888
closed
2 years ago
0
[ETL-168] Add structural variant class
#452
thomasyu888
closed
2 years ago
0
Create Release 13.1.1
#451
thomasyu888
closed
2 years ago
0
year or int of death is not applicable for living patients
#450
hhunterzinck
closed
2 years ago
0
Modify check for DEAD variable in clinical file
#449
hhunterzinck
closed
2 years ago
0
Add code of conduct
#448
thomasyu888
closed
2 years ago
0
Release v13.0.0
#447
thomasyu888
closed
2 years ago
0
Update pandas version
#446
thomasyu888
closed
2 years ago
0
Fix Docker build
#445
thomasyu888
closed
2 years ago
0
[IBCDPE-149] Implement new SAMPLE_ID validation
#444
thomasyu888
closed
2 years ago
3
Add validation check for SAMPLE_ID
#443
hhunterzinck
closed
2 years ago
1
Docker build not working
#442
thomasyu888
closed
2 years ago
0
Add sample class filter
#441
thomasyu888
closed
2 years ago
0
[ETL-134] Use pandera
#440
thomasyu888
closed
1 year ago
0
Add check year
#439
thomasyu888
closed
2 years ago
2
Modify tsa1, tsa2, ref maf error message
#438
thomasyu888
closed
2 years ago
0
fixes to seq-assay-id validation checks
#437
hhunterzinck
closed
2 years ago
9
make seq_assay_id check case insensitive
#436
hhunterzinck
closed
2 years ago
3
Make validation of SEQ_ASSAY_IDs case-insensitive
#435
hhunterzinck
closed
2 years ago
1
Modify error message for maf.py check
#434
hhunterzinck
closed
2 years ago
0
Revise dashboards
#433
thomasyu888
closed
2 years ago
0
Fix the GENIE install for the docker image
#432
thomasyu888
closed
2 years ago
0
Don't cache local install
#431
thomasyu888
closed
2 years ago
0
Fix installation for python packages
#430
thomasyu888
closed
2 years ago
0
Add to cli
#429
thomasyu888
closed
2 years ago
0
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