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TCP-Lab
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transportome_profiler
Code to profile the expression of the transportome
GNU General Public License v3.0
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Wrong query in `basic.json`
#41
Feat-FeAR
closed
1 week ago
1
In `make_genesets.py`, the parameter `min_pop_score` works the other way around
#40
Feat-FeAR
closed
1 week ago
1
Extract ENSG-HGNC ID correspondences from the MTP-DB
#39
Feat-FeAR
closed
1 week ago
2
Update cancer types for DEA
#38
MrHedmad
closed
1 week ago
4
Add shared dysregulation plot
#37
MrHedmad
closed
2 weeks ago
0
Comment why this specific metric was used
#36
MrHedmad
closed
1 week ago
1
Add GEO datasets
#35
MrHedmad
closed
8 months ago
0
Have reliable pruning
#34
MrHedmad
closed
8 months ago
1
Non-deterministic (nor reproducible) pruning.
#33
Feat-FeAR
closed
7 months ago
3
Mention the dependency on `jq` in the README
#32
Feat-FeAR
closed
9 months ago
1
Missing reference to `fast-cohen` dependency
#31
Feat-FeAR
closed
9 months ago
0
Cleanup selection of tumor types
#30
MrHedmad
closed
9 months ago
0
Review of the queries for the TCGA-GTEX pairing.
#29
Feat-FeAR
closed
9 months ago
1
Redundancy in `dea_queries.json`
#28
Feat-FeAR
closed
9 months ago
1
Cannot run the `heatmaps` pipeline on "test espression matrix"
#27
Feat-FeAR
closed
10 months ago
1
Bad hardcoded output path in `metasample.py`
#26
Feat-FeAR
closed
10 months ago
2
Rewrite plotting functions
#25
MrHedmad
closed
10 months ago
0
Migrate to Kerblam!
#24
MrHedmad
closed
10 months ago
0
The Log Fold Change calculation is wrong
#23
MrHedmad
closed
10 months ago
0
The DESeq2 Fold Change computation is too slow
#22
MrHedmad
closed
10 months ago
0
Code review
#21
MrHedmad
closed
9 months ago
2
Add pipeline documentation
#20
MrHedmad
closed
10 months ago
0
Create a Log2FC heatmap
#19
MrHedmad
closed
7 months ago
0
Cancer types are not well defined
#18
MrHedmad
closed
1 week ago
0
Find independent tumor/healthy data
#17
MrHedmad
closed
4 months ago
0
Extract metastatic samples
#16
MrHedmad
closed
1 week ago
0
Stratify the analysis with clinical variables
#15
MrHedmad
closed
4 months ago
2
Redefine the metasplit calls to be more specific
#14
MrHedmad
closed
1 week ago
0
Make the MTP-DB release static
#13
MrHedmad
closed
7 months ago
1
Use a better structure for the geneset graph
#12
MrHedmad
closed
7 months ago
1
No way to add custom genesets
#11
MrHedmad
closed
4 months ago
1
Add extra data for verification
#10
MrHedmad
closed
9 months ago
1
Using the t-statistic is not completely correct
#9
MrHedmad
closed
1 year ago
0
Pre-preprint changes
#8
MrHedmad
closed
1 year ago
1
Update in the paper all the old CMA-Lab urls to the newest TCP-Lab equivalents
#7
Feat-FeAR
closed
1 year ago
1
Using Xena directly may not be reproducible
#6
MrHedmad
closed
7 months ago
1
Adapt to the new MTP-DB
#5
MrHedmad
closed
1 year ago
0
To deseq
#4
MrHedmad
closed
1 year ago
0
Better to use DESeq2 for logFC calculation
#3
Feat-FeAR
closed
1 year ago
1
Choen implementation
#2
MrHedmad
closed
1 year ago
0
fgsea returns NAs when using cohen's D
#1
MrHedmad
closed
1 year ago
1