AlexsLemonade OpenPBTA-analysis issues

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

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Updated data-formats.md

#1160 kgaonkar6 closed 3 years ago
1
#1144 part1: Interaction plot updated to cancer_groups

#1159 kgaonkar6 closed 3 years ago
2
[Figures]: update `figures` README with theme and cancer group info

#1158 jharenza closed 3 years ago
1
Data release v21

#1157 kgaonkar6 closed 3 years ago
1
PBTA histologies v21: PR1 Include SEGA to molecular-subtyping-LGAT

#1156 kgaonkar6 closed 3 years ago
1
Update broad/short histology matching in base histologies file

#1155 kgaonkar6 closed 3 years ago
1
Updated analysis: Add pathology_diagnosis == Subependymal Giant Cell Astrocytoma (SEGA) to LGAT

#1154 kgaonkar6 closed 3 years ago
1
add boxplots by molecular subtypes

#1153 komalsrathi closed 3 years ago
7
add p53 classifier plots 1/n

#1152 jharenza closed 3 years ago
1
tp53 classifier plots 1/n

#1151 jharenza closed 3 years ago
1
PBTA histologies v21: PR2 Update GNG, GNT and SEGA sample integrated_diagnosis

#1150 kgaonkar6 closed 3 years ago
7
v21 release: minor histology file update

#1149 jharenza closed 3 years ago
2
Updated analysis: update oncoprint panel figure code

#1148 jharenza closed 3 years ago
2
oncoprint update PR 2/n replace display group with cancer_group

#1147 kgaonkar6 closed 3 years ago
1
Updated analysis: tp53 module to add figures for manuscript

#1146 jharenza closed 3 years ago
5
Updated analysis: telomerase activity by subtypes

#1145 jharenza closed 3 years ago
1
Updated analysis: update some figures to include annotations by `cancer_group` for manuscript

#1144 jharenza closed 2 years ago
9
oncoprint update PR 1/n

#1143 jharenza closed 3 years ago
2
Hex code update from adding cancer_group as display_group

#1142 kgaonkar6 closed 3 years ago
10
Updated analysis: oncoprint-landscape

#1141 kgaonkar6 closed 3 years ago
6
Updated analysis: figures/mapping-histology-labels.Rmd

#1140 kgaonkar6 closed 3 years ago
1
Updated analysis: update all modules to use v21 data for release v1

#1139 jharenza closed 2 years ago
1
rerun immune deconv with v20 data

#1138 jharenza closed 3 years ago
0
Updated analysis: rerun `immune-deconv` with v20 data

#1137 jharenza closed 3 years ago
1
rerun `chr-cnv-plot` with v20

#1136 jharenza closed 3 years ago
0
Updated analysis: rerun cnv-chrom-plot with v20 data release

#1135 jharenza closed 3 years ago
1
filter manta == PASS and rerun chr-instability using v20 data

#1134 jharenza closed 3 years ago
0
Updated analysis: add manta PASS filter to chr instability and rerun with v20

#1133 jharenza closed 3 years ago
1
Updated analysis: regenerate figures using v21 data release

#1132 jharenza closed 2 years ago
2
remove previous CNV results to force full snakemake run in CI

#1131 jashapiro closed 3 years ago
3
Update focal-cn-preparation to use consensus SEG file in data download

#1130 jaclyn-taroni closed 3 years ago
3
Focal CN preparation takes over an hour to run in CI

#1129 jaclyn-taroni closed 3 years ago
1
V20 PBTA histologies: Add cancer group

#1128 kgaonkar6 closed 3 years ago
3
v20 CNV update part4 : Rerun gistic and molecular subtyping v20

#1127 kgaonkar6 closed 3 years ago
15
V20 CNV update part3: TP53 alteration update

#1126 kgaonkar6 closed 3 years ago
0
Proposed Analysis: Review 50% reciprocal overlap in CNV consensus analysis

#1125 kgaonkar6 closed 3 years ago
1
V20 CNV update part2: focal cnv and oncoprint rerun

#1124 kgaonkar6 closed 3 years ago
3
V20 CNV update part1: Update overlap criteria for consensus CNV

#1123 kgaonkar6 closed 3 years ago
8
Updated analysis: chromothripsis

#1122 kgaonkar6 closed 3 years ago
7
change to kf-openaccess-us-east-1-prd-pbta/data

#1121 kgaonkar6 closed 3 years ago
10
V20 ci files

#1120 kgaonkar6 closed 3 years ago
1
Outdated PBTA Histologies v20 : Run molecular subtyping

#1119 kgaonkar6 closed 3 years ago
1
Download data v20

#1118 kgaonkar6 closed 3 years ago
4
Adding str_detect to fix issue with EMTR

#1117 kgaonkar6 closed 3 years ago
0
Update manta FILTER=='PASS' Part3 : oncoprint rerun

#1116 kgaonkar6 closed 3 years ago
5
Update manta FILTER=='PASS' Part2 : gene annotated cnv file generation

#1115 kgaonkar6 closed 3 years ago
0
Update manta FILTER=='PASS' Part1 : consensus cnv file generation

#1114 kgaonkar6 closed 3 years ago
1
Updated analysis: Subset manta FILTER=="PASS" consensus cnv

#1113 kgaonkar6 closed 3 years ago
1
Fix the number of palettes in the figures README

#1112 jaclyn-taroni closed 3 years ago
1
Update pathology feedback for BS_H1XPVS9A

#1111 jharenza closed 3 years ago
2

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