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d3b-center
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PBTA-ALT-analysis
Repository for CBTTC-ALT project with Kristina Cole
MIT License
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#65
jharenza
closed
2 years ago
0
Atrx clonality exploration
#64
jharenza
closed
2 years ago
2
add missing dependencies to dockerfile
#63
jharenza
closed
2 years ago
0
add command line option for oncokb annotation
#62
rjcorb
closed
2 years ago
3
Update lollipop
#61
rjcorb
closed
2 years ago
1
add VAF to oncoKB PBTA maf file
#60
jharenza
closed
2 years ago
0
Updated analysis: Create command line arguments for oncoKB token
#59
jharenza
closed
2 years ago
2
add TERT to oncoprint
#58
jharenza
closed
2 years ago
1
rerun survival analysis with K28-altered cohort
#57
jharenza
closed
2 years ago
1
Updates for revision
#56
jharenza
closed
2 years ago
0
add file to merge cancer groupings with figure 1
#55
jharenza
closed
2 years ago
0
export data table for figure S1
#54
jharenza
closed
2 years ago
0
Update table s1
#53
jharenza
closed
2 years ago
0
Update README.md
#52
jharenza
closed
2 years ago
0
Add table s1
#51
jharenza
closed
2 years ago
0
create Table S4
#50
jharenza
closed
2 years ago
0
add mut sigs to df
#49
jharenza
closed
2 years ago
0
Add Shuffle ROC, update germline list
#48
jharenza
closed
2 years ago
0
WIP: Required docker updates
#47
jharenza
closed
2 years ago
1
🎉 add analysis Dockerfile
#46
dmiller15
closed
2 years ago
0
counts and freq for all genes by oncogenicity
#45
jharenza
closed
2 years ago
0
What is the best way to run ROCs for ALT?
#44
jharenza
closed
2 years ago
9
Create docker image for repo
#43
jharenza
closed
2 years ago
2
Create PBTA telhunt distribution plot for S1
#42
jharenza
closed
2 years ago
1
Tiff figs - updates for manuscript
#41
jharenza
closed
2 years ago
0
Check tmb
#40
jharenza
closed
2 years ago
0
update oncoprint
#39
jharenza
closed
2 years ago
0
Use `alt final` instead of phenotype
#38
runjin326
closed
2 years ago
1
Add lollipop plots
#37
jharenza
closed
2 years ago
0
add survival analysis
#36
jharenza
closed
2 years ago
0
rerun 07 scripts, add count_df out
#35
jharenza
closed
2 years ago
0
rerun 05 oncoprint
#34
jharenza
closed
2 years ago
0
rerun 04 script - cutpoint analysis
#33
jharenza
closed
2 years ago
1
rerun 03 script
#32
jharenza
closed
2 years ago
0
Reruns for jenny - add new files and add rerun 02
#31
jharenza
closed
2 years ago
0
Updated analysis: re-run all analyses with non-HGAT data as well
#30
runjin326
closed
2 years ago
1
Raw data for tumor mutational burden analysis
#29
jstundon
closed
2 years ago
3
Proposed Analysis: Lollipop of ATRX mutations in ALT+/ALT- HGAT patients
#28
jstundon
closed
2 years ago
3
Four new figures added separated by ATRX
#27
runjin326
closed
2 years ago
3
Proposed Analysis: is increased somatic mutational burden seen in ALT+ HGAT independent of ATRX status?
#26
jstundon
closed
2 years ago
4
compile figures
#25
jharenza
closed
2 years ago
3
Panel C Frequency Stacked Bar Plot
#24
runjin326
closed
2 years ago
2
Bar plot with percentage mutations
#23
runjin326
closed
2 years ago
4
Mutation Count Boxplots
#22
runjin326
closed
2 years ago
6
Oncoprint update
#21
runjin326
closed
2 years ago
3
Re-run all analyses
#20
runjin326
closed
2 years ago
0
Proposed Analysis: assess molecular subtypes between ALT+/- groups
#19
jharenza
closed
2 years ago
1
Proposed Analysis: assess N samples with specific gene mutations by ALT status
#18
jharenza
closed
2 years ago
1
Proposed Analysis: mutation count differences between ALT+/- patients
#17
jharenza
closed
2 years ago
1
Updated analysis: update oncoprint
#16
jharenza
closed
2 years ago
1
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