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Sage-Bionetworks
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Genie
Validation and processing of GENIE files
https://genie.synapse.org/
MIT License
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fix: update maf read_csv
#528
jakevc
closed
1 year ago
2
[GEN-720] support new SV primary keys
#527
thomasyu888
closed
1 year ago
0
Do not cross-file validate if ancillary files not present
#526
thomasyu888
closed
1 year ago
0
Add in support for ancilliary files in cli
#525
thomasyu888
closed
8 months ago
1
[GEN-706] Cross-validate clinical assay information
#524
rxu17
closed
1 year ago
1
[GEN-561] Add cross validation to check for seq-assay-id bed file pair
#523
rxu17
closed
1 year ago
1
[GEN-562] Cross-validate maf with clinical sample files
#522
rxu17
closed
1 year ago
2
Add mypy pre-commit
#521
thomasyu888
closed
1 year ago
1
[GEN-560] Add ancillary files for cross-validation
#520
rxu17
closed
1 year ago
0
[GEN-694] Remove fusions from dashboarding
#519
thomasyu888
closed
1 year ago
0
[GEN-81] Deprecate support for passwords, and authentication parameters in cli
#518
thomasyu888
closed
1 year ago
0
Add in pre-commit
#517
thomasyu888
closed
1 year ago
0
[GEN-636] Allow NAs/blanks for unrequired columns in SV
#516
rxu17
closed
1 year ago
0
[GEN-564] Add support for more values for site1 site2 col in SV file
#515
rxu17
closed
1 year ago
0
[GEN-493] Accept Unknown for SV dna and rna support columns
#514
rxu17
closed
1 year ago
0
Dashboard code should support multiple major public releases, but always new the latest
#513
thomasyu888
closed
1 year ago
0
MAF file validation
#512
jakevc
opened
1 year ago
1
[GEN-568] Create sv case list
#511
rxu17
closed
1 year ago
0
[GEN-429] Validate chromosome columns in bed file
#510
rxu17
closed
1 year ago
1
[GEN-428] Validate chromosome column in SV
#509
rxu17
closed
1 year ago
0
15.1.0-rc
#508
thomasyu888
closed
1 year ago
0
[GEN-496] remove fusions file support
#507
rxu17
closed
1 year ago
0
[GEN-506] Support new synapser client - Update installation
#506
thomasyu888
closed
1 year ago
0
[GEN-497] Remove fusion file from consortium release
#505
thomasyu888
closed
1 year ago
0
[GEN-461] Hotfix - fix processing, invalid syn.tableQuery and wrong sv column headers
#504
thomasyu888
closed
1 year ago
0
[GEN-445] Allow for NA values SV files
#503
thomasyu888
closed
1 year ago
0
[GEN-427] Use validation_chrom function for maf
#502
thomasyu888
closed
1 year ago
1
[GEN-426] Use new function to validate chromosome for SEG file
#501
thomasyu888
closed
1 year ago
1
[GEN-290] Write dup variants
#500
thomasyu888
closed
1 year ago
1
[GEN-424, GEN-423] Allow MT chromosome to be specified
#499
thomasyu888
closed
1 year ago
0
[GEN-416] Pin dependency versions
#498
thomasyu888
closed
1 year ago
0
[GEN-407] Check GENIE genome nexus instance
#497
thomasyu888
closed
1 year ago
0
[GEN-258] Update SV validation
#496
thomasyu888
closed
1 year ago
0
[GEN-413] Update GENIE VCF validation
#495
thomasyu888
closed
1 year ago
0
[GEN-413] Add more vcf validation rules
#494
thomasyu888
closed
1 year ago
0
[GEN-412] Add renv and better installation/testing instructions
#493
thomasyu888
closed
1 year ago
0
[GEN-299] add load module
#492
thomasyu888
closed
1 year ago
0
[GEN-324] use conftest throughout tests
#491
thomasyu888
closed
1 year ago
1
[GEN-323] remove unused classes
#490
thomasyu888
closed
1 year ago
0
[GEN-295] Add extract.py module
#489
thomasyu888
closed
1 year ago
0
[GEN-285] hotfix - make sure release folder fileview is indexed
#488
thomasyu888
closed
1 year ago
0
[GEN-258] Update structural variant validation
#487
thomasyu888
closed
1 year ago
0
Prepare release 14.3.0
#486
thomasyu888
closed
1 year ago
0
v14.3.0 release candidate
#485
thomasyu888
closed
1 year ago
0
[GEN-76] No longer need to include the release version in the release files
#484
thomasyu888
closed
1 year ago
0
[GEN-185] Fusions entrez gene must be integers
#483
thomasyu888
closed
1 year ago
0
[GEN-177] HOTFIX - Lock down pandas version
#482
thomasyu888
closed
1 year ago
0
[GEN-174] allow for patch public release versions to be specified
#481
thomasyu888
closed
1 year ago
0
[GEN-33] Support sv format
#480
thomasyu888
closed
1 year ago
0
[GEN-95] Make sure to add simple table query to re-index file view
#479
thomasyu888
closed
1 year ago
0
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