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broadinstitute
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PANOPLY
Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
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Running proteomics only analysis, error in validate_input(): ERROR. Genomics data (cna/rna) missing
#45
sooheon
opened
1 month ago
0
Azurize panoply_fragpipe_search WDL (with tarred input file)
#44
aawdeh
opened
4 months ago
0
Azurize panoply_fragpipe_search WDL
#43
aawdeh
closed
4 months ago
1
Following tutorial with V1.3, run_panda() does not populate data
#42
sooheon
closed
5 months ago
3
Updated documentation for DIA-NN and Skyline viz
#41
Munchic
closed
1 year ago
0
Can we use Singularity (not docker) to analysis it ?
#40
TrumanZYX
closed
1 year ago
1
[small updates] Raw proteomics processing
#39
Munchic
closed
1 year ago
0
FragPipe and DIA-NN Terra workflows from raw proteomics processing
#38
Munchic
closed
1 year ago
0
Raw proteomics processing
#37
Munchic
closed
1 year ago
0
(Document update) panoply_cna_setup and panoply_cna_correlation
#36
hsiaoyi0504
closed
2 years ago
1
Initialization cell in PANOPLY-startup-notebook never finishes
#35
wnojopra
closed
2 years ago
2
The source R files in R-utiliites
#34
wangshisheng
closed
2 years ago
4
Made GSEA plotting robust against missing files.
#33
wcorinne
closed
2 years ago
0
Issue blacksheepannot
#32
wcorinne
closed
2 years ago
0
fix the script name in panoply_ssgsea_report
#31
hsiaoyi0504
closed
2 years ago
3
Alphabet function
#30
hsiaoyi0504
closed
2 years ago
2
How to normalize CNA and RNA data before NMF? What is the normalization method in the example data
#29
SepOrion
closed
2 years ago
1
Issue add quilts
#28
mmaynard-source
closed
3 years ago
0
Update panoply_unified_workflow.wdl
#27
mmaynard-source
closed
3 years ago
0
Issue separate normalize
#26
mmaynard-source
closed
3 years ago
0
Issue yaml parameters
#25
mmaynard-source
closed
4 years ago
0
Issue unified panoply
#24
ramanibk
closed
4 years ago
0
SGT Enabled
#23
ramanibk
closed
4 years ago
0
(PANDA) parameters.yaml
#22
ramanibk
closed
4 years ago
1
(PANDA) retrieve existing color scheme
#21
ramanibk
closed
4 years ago
1
(PANDA) _copy to _<num>
#20
ramanibk
closed
4 years ago
1
PANDA Notebook and Tool Merge
#19
ramanibk
closed
4 years ago
0
Issue release
#18
ramanibk
closed
4 years ago
0
Issue rebrand
#17
ramanibk
closed
4 years ago
1
Issue rebrand
#16
ramanibk
closed
4 years ago
0
Retain "VMsiteFlanks" column in the GCT files
#15
karstenkrug
closed
4 years ago
2
Renamed tasks from pgdac_* to pnaoply_*
#14
ramanibk
closed
4 years ago
0
Resolve gct-io.r vs. cmapR conflict
#13
ramanibk
closed
4 years ago
0
SGT handling function is not being called in pgdac_harmonize
#12
ramanibk
closed
4 years ago
1
Clustering: Automatically adjust SD threshold to ensure sufficient markers
#11
drmani
closed
4 years ago
0
Include license in WDL files
#10
drmani
closed
4 years ago
0
Improve error checking
#9
drmani
closed
4 years ago
0
Incorporate FireCloud data model
#8
drmani
closed
4 years ago
1
Improve run-pipeline.sh script
#7
drmani
closed
4 years ago
0
Improve docker build
#6
drmani
closed
5 years ago
1
Document tasks and workflows
#5
drmani
closed
5 years ago
0
Add tests for all tasks and workflows
#4
drmani
closed
4 years ago
1
Migrate tasks/workflow to Hydrant
#3
drmani
closed
5 years ago
1
Fix NMF clustering in pgdac_main
#2
drmani
closed
6 years ago
1
Add FireCloud method for each pipeline task
#1
drmani
closed
6 years ago
1