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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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Updated analysis: survival analysis generalization
#1210
runjin326
closed
2 years ago
1
Revamp `figures` documentation
#1209
jaclyn-taroni
closed
2 years ago
1
Add survival curves by TP53 and telomerase scores
#1208
jharenza
closed
2 years ago
13
V22 data release
#1207
jharenza
closed
2 years ago
0
add molecular subtype to wgs-only samples
#1206
komalsrathi
closed
2 years ago
4
Update TP53 classifier plots by broad histology and cancer group to fit new conventions
#1205
jaclyn-taroni
closed
2 years ago
1
CI calculation added for odds ratio
#1204
runjin326
closed
2 years ago
3
Updated analysis: Add CI to interaction-plots module
#1203
runjin326
closed
2 years ago
1
Tp53 figures by broad histology and cancer group
#1202
jharenza
closed
2 years ago
0
New sample distribution main & supplemental display items
#1201
jaclyn-taroni
closed
2 years ago
8
OncoPrint figures
#1200
jaclyn-taroni
closed
2 years ago
9
tables and script added
#1199
runjin326
closed
2 years ago
4
Proposed Analysis: Create tsnes with molecular subtype highlighted for Fig S4
#1198
jharenza
closed
2 years ago
3
Update interaction plot to use new cancer group palette
#1197
jaclyn-taroni
closed
2 years ago
2
Update chromothripsis panels to use new cancer group palette (Fig 3)
#1196
jaclyn-taroni
closed
2 years ago
1
Add Figure 1A component
#1195
jaclyn-taroni
closed
2 years ago
0
Update Figure 4 single panel PDFs, add compiled figure
#1194
jaclyn-taroni
closed
2 years ago
0
Create minimal main display item palette (#1176)
#1193
jaclyn-taroni
closed
2 years ago
4
Take "sufficiently non-zero" approach to exposures for CNS signature fitting
#1192
jaclyn-taroni
closed
2 years ago
0
Oncoprint output count tables
#1191
runjin326
closed
2 years ago
5
Save output of fit_signatures(), make it easier just to run CNS fitting steps
#1190
jaclyn-taroni
closed
2 years ago
0
N per cancer_group oncoprint
#1189
kgaonkar6
closed
2 years ago
0
add Ns and percents to co-occurrence tables for paper
#1188
jharenza
closed
2 years ago
1
Proposed Analysis: Create manuscript tables
#1187
jharenza
closed
2 years ago
1
Add v21 combined data matrices to s3 for pedcbio load
#1186
jharenza
closed
2 years ago
1
Add OpenPBTA v21 (GitHub release 1) publication study to PedcBio
#1185
jharenza
closed
2 years ago
27
Updated analysis: oncoprint landscape missing SMARCB1 for embryonal (ATRT)
#1184
jharenza
closed
2 years ago
5
Updated analysis: medullo subtyping misses WGS only samples as To be Classified
#1183
jharenza
closed
2 years ago
3
Updated analysis: oncoprint readme/output to list Ns per group
#1182
jharenza
closed
2 years ago
4
Ind samples update
#1181
komalsrathi
closed
2 years ago
0
Updated analysis: GISTIC with ploidy instead of NA
#1180
kgaonkar6
closed
2 years ago
3
Idea: Create co-occurrence plots per cancer group, assemble into multipanel figure
#1179
jaclyn-taroni
closed
3 years ago
2
Create panel of standalone legends for the oncoprint plots
#1178
jaclyn-taroni
closed
2 years ago
1
Updated analysis: Oncoprints to use new minimal display palettes, remove cancer group with n < 10
#1177
jaclyn-taroni
closed
2 years ago
4
Update figures/ to reflect new minimal "display group" palettes
#1176
jaclyn-taroni
closed
2 years ago
1
Split up sample distribution representation between figures and tables, main text and supplement
#1175
jaclyn-taroni
closed
2 years ago
3
Rework cancer group / display group palettes to identify a minimal number of colors for multi-group display
#1174
jaclyn-taroni
closed
3 years ago
14
[Discussion] - Manuscript figure for de novo mutational signatures
#1173
jharenza
closed
2 years ago
3
update figures README
#1172
jharenza
closed
3 years ago
0
#1144 part 4 Rerun transcriptomics fig generation with cancer_group for UMAP
#1171
kgaonkar6
closed
3 years ago
10
Chromothripsis v21 update
#1170
LauraEgolf
closed
3 years ago
4
Update EPN subtyping readme
#1169
jashapiro
closed
3 years ago
0
#1144 part3 update telomerase activities figure
#1168
kgaonkar6
closed
3 years ago
2
#1144 Part 3: Telomerase activity prediction hex update
#1167
kgaonkar6
closed
3 years ago
1
Update tp53 module to add figures for manuscript
#1166
komalsrathi
closed
3 years ago
10
Updated analysis: oncoprint update aesthetics
#1165
jharenza
closed
3 years ago
2
Update oncoprint panel figure
#1164
cbethell
closed
3 years ago
9
update OpenPBTA bucket
#1163
jharenza
closed
3 years ago
0
Create new bucket and update path
#1162
jharenza
closed
3 years ago
1
#1144 part2: Sample distribution multi-layer plot
#1161
kgaonkar6
closed
3 years ago
8
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