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d3b-center
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OpenPedCan-analysis
The analysis repository for the Open Pediatric Cancer Project
https://d3b-center.github.io/OpenPedCan-analysis/
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rerun tables for manuscript
#596
jharenza
closed
9 hours ago
1
rerun author contributions for biorxiv submission - as of July 9
#595
jharenza
closed
9 hours ago
1
Rjcorb/569 mb shh umap
#594
rjcorb
closed
10 hours ago
1
Pathology review of MB samples with high-conf other subtypes needed
#593
jharenza
opened
2 days ago
0
HOPE tumor_only sub_cohort missing `germline_sex_estimate` annotation as "Unknown"
#592
jharenza
opened
2 days ago
0
CNV consensus w freec wxs
#591
jharenza
closed
4 hours ago
1
Updated analysis: add PPTID to PB subtyping
#590
jharenza
opened
1 week ago
0
Updated analysis: consensus CN - XY chrs have artifactual calls
#589
jharenza
closed
4 hours ago
2
Update manuscript: Generate tables
#588
zzgeng
closed
1 week ago
0
Check DIPG cancer groupings
#587
jharenza
opened
1 week ago
0
Add treatment info to V16
#586
migbro
opened
3 weeks ago
0
Rokita/author template
#585
jharenza
closed
3 weeks ago
1
add compiled figure, rerun
#584
jharenza
closed
3 weeks ago
0
Manuscript: Add percentage to pie chart
#583
zzgeng
closed
4 weeks ago
1
remove gitignore til GHA works
#582
jharenza
closed
2 days ago
1
update branch to dev for contributions yaml job
#581
jharenza
closed
1 month ago
0
Generate plot/counts for the manuscript
#580
zzgeng
closed
1 month ago
3
Collect the list for packages/software version
#579
zzgeng
closed
1 month ago
1
Create workflow to update yaml file for manuscript
#578
jharenza
closed
1 month ago
0
Updated analysis: add exome capture samples to testing data
#577
jharenza
opened
1 month ago
0
⚰️ Remove pull_request condition from build workflow
#576
devbyaccident
closed
1 month ago
0
update build token/user and docker packages
#575
jharenza
closed
1 month ago
0
Upgrade snakemake
#574
sickler-alex
closed
1 month ago
1
Module contribution counts
#573
jharenza
closed
1 month ago
2
re-org docker file, upgrades
#572
jharenza
closed
2 months ago
0
move analysis module action
#571
jharenza
closed
1 month ago
1
add UMAP script
#570
rjcorb
closed
17 hours ago
2
Updated analysis: add code to generate methylation UMAP for MB SHH samples
#569
rjcorb
closed
10 hours ago
0
update R and bioconductor versions
#568
jharenza
closed
2 months ago
0
Update rocker tidyverse version to R4.4.0 following vulnerability report
#567
jharenza
closed
2 months ago
0
Updated analysis: BS_YZD4SSMA has cancer group DIPG, but DMG subtype
#566
jharenza
opened
2 months ago
0
MB SHH subtyping
#565
rjcorb
closed
17 hours ago
4
Proposed Analysis: Medulloblastoma SHH subtyping
#564
jharenza
closed
17 hours ago
0
Updated analysis: TMB calculation for tumor only WGS
#563
jharenza
closed
2 days ago
1
👯♀️ Slightly duplicated RNA_library
#562
migbro
opened
3 months ago
1
Add `biospecimen_site` or other field designation for autopsy sample locations
#561
jharenza
opened
3 months ago
0
Add missing samples to tmb calculation files
#560
jharenza
closed
3 months ago
2
DGD sample duplications in `histologies.tsv`
#559
jharenza
opened
4 months ago
1
Duplicates in `fusion-annoFuse.tsv.gz` file
#558
jharenza
opened
4 months ago
1
`cnv-controlfreec-tumor-only.tsv.gz` status field capitalized but other CNV files lowercase
#557
jharenza
opened
4 months ago
2
update runs to checkout@v4 to use node20 since node16 is deprecated
#556
jharenza
closed
4 months ago
0
V15 subset files (2/2)
#555
jharenza
closed
4 months ago
0
V15 download and release notes (1/2)
#554
jharenza
closed
4 months ago
0
🐛 Fix Collapse bug
#553
migbro
closed
4 months ago
1
D3b Bix Dev Feature: Fix bug
#552
migbro
closed
4 months ago
1
v15 data release - update TCGA and GTEX count and TPM matrices
#551
jharenza
closed
4 months ago
1
D3b Bix Dev Feature: Change Docker image
#550
migbro
closed
4 months ago
1
Missing TCGA counts from v14
#549
komalsrathi
closed
4 months ago
14
Update data-files-description to add miRNA file
#548
jharenza
closed
4 months ago
1
Pull survival module from OpenPBTA
#547
jharenza
closed
5 months ago
3
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