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d3b-center
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ticket-tracker-OPC
A repo to generate and track tickets for ped OT
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Update workflow scripts associated with the data release analysis process
#561
ewafula
closed
1 year ago
1
Remove sample not-consented from methyl matrices
#559
ewafula
closed
1 year ago
3
Updated snakemake workflow for copy_number_consensus_call module
#557
ewafula
closed
1 year ago
31
Rerun all of the modules with the new docker image
#556
ewafula
closed
1 year ago
1
Create v13 RNA-Seq merged matrices
#555
jharenza
closed
1 year ago
1
Updated documentation: analysis README out of date
#554
jharenza
closed
1 year ago
9
Updated analysis: tmb calculation
#553
jharenza
closed
1 year ago
0
Missing germline sex estimate in ops csv
#552
jharenza
closed
1 year ago
7
Updated analysis: missing NBL samples in histologies file
#550
zzgeng
closed
1 year ago
1
The difference of variant call files for DNA sample between v11 and v12 release
#549
zzgeng
closed
1 year ago
2
Updated analysis: Refactoring molecular-subtyping-neurocytoma module
#546
zzgeng
closed
1 year ago
1
Updated analysis: Refactoring molecular-subtyping-Chordoma module
#545
zzgeng
closed
1 year ago
1
Updated analysis: Refactoring molecular-subtyping-EWS module
#544
zzgeng
closed
1 year ago
1
Updated analysis: Refactoring molecular-subtyping-EPN module
#543
zzgeng
closed
1 year ago
1
Updated analysis: Refactoring molecular-subtyping-CRANIO module
#542
zzgeng
closed
1 year ago
1
Updated analysis: Refactoring molecular-subtyping-ATRT module
#541
zzgeng
closed
1 year ago
1
Pull in EFS_event_type and update EFS_days
#540
jharenza
closed
1 year ago
1
Liftover Hotspot annotation to GENCODE v39 gene symbols
#539
jharenza
closed
1 year ago
1
Update to R version 4.2.3 in docker image
#537
jharenza
closed
1 year ago
3
Enrich CI testing subset data for +/- tp53 alterations
#536
ewafula
closed
1 year ago
0
Copy v12 OPC files into CAVATICA project
#535
jharenza
closed
1 year ago
2
Update debian sources list (possible issue)
#534
jharenza
closed
1 year ago
3
Updated analysis: Fusion filtering
#533
migbro
closed
1 year ago
2
Updated analysis: pedcbio-sample-name
#532
migbro
closed
1 year ago
9
Updated analysis: update embryonal subtyping TTYH1 fusion search
#531
jharenza
closed
1 year ago
1
update rna-seq-expression-summary-stats tables for v12
#530
ewafula
closed
1 year ago
1
update snv-frequencies tables for v12
#529
ewafula
closed
1 year ago
1
update fusion-frequencies tables for v12
#528
ewafula
closed
1 year ago
1
update cnv-frequencies tables for v12
#527
ewafula
closed
1 year ago
1
Updated efo-mondo-mapping module for v12 data release
#526
ewafula
closed
1 year ago
7
Update gene_match module for v12 data release
#525
ewafula
closed
1 year ago
2
Update BS_IDs in methly matrices
#524
ewafula
closed
1 year ago
4
Add germline sex estimate to bixops file
#523
jharenza
closed
1 year ago
2
Remap GTEx TPM matrix to GENCODE v39 gene symbols
#522
jharenza
closed
1 year ago
6
Remap TCGA expression matrix to GENCODE v39
#521
jharenza
closed
1 year ago
12
Updated harmonized pre-release data files
#520
ewafula
closed
1 year ago
45
Updated analysis: fusion-summary to include _all_ samples with RNA-Seq or fusion panel
#519
jharenza
closed
1 year ago
2
1123 samples missing `RNA_library`
#518
jharenza
closed
1 year ago
1
Cell line composition and cell line passage in v12 histologies - for v12 subtyping
#517
jharenza
closed
1 year ago
2
Li-Fraumeni syndrome ----> Li-Fraumeni syndrome (TP53) in v12
#516
jharenza
closed
1 year ago
2
Add vroom to docker image after v12
#515
jharenza
closed
1 year ago
0
Updated analysis: CN file preparation
#514
aadamk
closed
1 year ago
1
Add methyl file download scripts to only relevant methylation modules
#513
jharenza
closed
1 year ago
1
Updated filter-mtp-tables module
#511
ewafula
closed
1 year ago
1
Updated MTP tables datatypeId column
#510
ewafula
closed
1 year ago
0
Bix Dev PedcbioPortal Support: OpenPedCan v12 on pedcbio
#509
ewafula
closed
1 year ago
36
Updated analysis: fusion filtering - modify artifact column selection for GTEx
#507
jharenza
closed
1 year ago
0
Updated analysis: Fusion frequencies to use DGD fusion file in `data/`
#506
jharenza
closed
1 year ago
1
Methylation column updates in v12+ `histologies.tsv`
#505
jharenza
closed
1 year ago
1
Updated analysis: Update mol subtyping integrate to include ATRT + NBL
#504
jharenza
closed
1 year ago
1
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