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AlexsLemonade
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OpenPBTA-analysis
The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Add a module for counting git contributions to the repository
#1410
jaclyn-taroni
closed
2 years ago
1
add missing key resources to software table S5
#1409
jharenza
closed
2 years ago
4
add sample Ns notebook
#1408
jharenza
closed
2 years ago
0
Updated analysis: tables/Key Resources
#1407
jharenza
closed
2 years ago
1
Update the shell scripts in `snv-callers` to have a consistent working directory
#1406
jaclyn-taroni
closed
2 years ago
0
WIP: Splitting analysis file generation and subtyping up
#1405
jaclyn-taroni
closed
2 years ago
1
Remove short histology from TMB function grouping
#1404
jaclyn-taroni
closed
2 years ago
1
Update HGG and LGG wording in figures
#1403
sjspielman
closed
2 years ago
2
Version update
#1402
runjin326
closed
2 years ago
1
Update broad histology and cancer group palettes, etc. to reflect v22 release
#1401
jaclyn-taroni
closed
2 years ago
13
Use ploidy for copy.num when running GISTIC
#1400
jaclyn-taroni
closed
2 years ago
0
Create bash script for generating analysis files, separate out subtyping steps
#1399
jaclyn-taroni
closed
2 years ago
3
Add Interaction sample calculation notebook
#1398
jharenza
closed
2 years ago
3
Rerun transcriptomic dimension reduction module
#1397
jaclyn-taroni
closed
2 years ago
4
Add clean = TRUE to EWS notebook rendering
#1396
jaclyn-taroni
closed
2 years ago
0
Update deploy step to use a specified Ubuntu image
#1395
jaclyn-taroni
closed
2 years ago
2
Change logic to use module data when generating figures
#1394
jaclyn-taroni
closed
2 years ago
1
Update compiled Figure 3
#1393
sjspielman
closed
2 years ago
2
Establish notebook for overall project sample sizes
#1392
sjspielman
closed
2 years ago
2
Establish notebook for interaction plots sample sizes
#1391
sjspielman
closed
2 years ago
2
Ensure figures adhere to submission guidelines
#1390
sjspielman
closed
2 years ago
1
Pre-V22 PR summary
#1389
jharenza
closed
2 years ago
1
Rerun subtype integrate post path update (2/2)
#1388
jharenza
closed
2 years ago
0
update pathology free text for LGAT (1/2)
#1387
jharenza
closed
2 years ago
2
Rerun molecular subtype integrate (10 of N)
#1386
jharenza
closed
2 years ago
0
Rerun molecular subtyping pathology (9 of N)
#1385
jharenza
closed
2 years ago
0
Rerun LGG subtyping (8 of N)
#1384
jharenza
closed
2 years ago
0
rerun tp53 module using RNA file in `/data`
#1383
jharenza
closed
2 years ago
2
Rerun hgg subtyping (7 of N)
#1382
jharenza
closed
2 years ago
1
Rerun neurocytoma (6 of N)
#1381
jharenza
closed
2 years ago
0
Rerun ews (5 of N)
#1380
jharenza
closed
2 years ago
1
rerun chordoma subtyping (4 of N)
#1379
jharenza
closed
2 years ago
2
rerun embryonal (3 of N)
#1378
jharenza
closed
2 years ago
1
Rerun EPN subtyping (2 of N)
#1377
jharenza
closed
2 years ago
1
update/rerun MB subtyping (1 of N)
#1376
jharenza
closed
2 years ago
2
rerun pathology_free_text-subtyping-lgat.Rmd
#1375
jharenza
closed
2 years ago
0
rerun MB subtyping with "MB, To be classified"
#1374
jharenza
closed
2 years ago
1
Update TP53 plot wording
#1373
sjspielman
closed
2 years ago
1
Update LGG plots
#1372
sjspielman
closed
2 years ago
2
Add "skip denovo" option for mutational signatures
#1371
sjspielman
closed
2 years ago
1
Add run script to GSVA module
#1370
sjspielman
closed
2 years ago
1
Create v22 CI files
#1369
jaclyn-taroni
closed
2 years ago
0
Updates required post v22 histologies file release
#1368
jharenza
closed
2 years ago
2
Rename Key Resources Table
#1367
sjspielman
closed
2 years ago
2
key resources table
#1366
sjspielman
closed
2 years ago
4
release V22
#1365
jharenza
closed
2 years ago
3
Compiled Figure S6
#1364
sjspielman
closed
2 years ago
0
Compiled Figure S5
#1363
sjspielman
closed
2 years ago
1
Add python3 tk to docker
#1362
sjspielman
closed
2 years ago
7
Add dependency: `python-tk`
#1361
sjspielman
closed
2 years ago
1
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