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cbg-ethz
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dce
Finding the causality in biological pathways
https://cbg-ethz.github.io/dce/
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using TCGAsplitAssays instead of deprecated splitAssays (BioC error)
#36
MartinFXP
closed
1 year ago
0
removed unused argument (na.value = 0.2)
#35
MartinFXP
closed
1 year ago
1
Add qqconf dependency
#34
kpj
closed
2 years ago
0
bioc
#33
kpj
closed
2 years ago
0
added arbitrary distributions for simulated data #25
#32
MartinFXP
closed
2 years ago
0
Update GTEx analysis to use TPM data
#31
dcevid
closed
2 years ago
0
added GTEx validation
#30
dcevid
closed
3 years ago
0
update latent simulation + citation
#29
MartinFXP
closed
3 years ago
0
Fix mysterious `Error: subscript out of bounds` crash
#28
kpj
closed
3 years ago
0
added CARNIVAL + differential gene expression and readded LDGM
#27
MartinFXP
closed
3 years ago
8
Deconfounding fix for real datasets
#26
dcevid
closed
3 years ago
1
Feature: add arbitrary distribution choice to simulate data
#25
MartinFXP
closed
2 years ago
2
bug in generating graph?
#24
dcevid
closed
3 years ago
5
Random DAG creation
#23
kpj
closed
3 years ago
0
Merge pathway nodes
#22
kpj
closed
3 years ago
1
TPM vs raw counts
#21
MartinFXP
closed
3 years ago
1
Open issues:
#20
MartinFXP
closed
4 years ago
3
List of relevant pathway enrichment tools
#19
kpj
closed
4 years ago
6
How to control the noise in (large) graphs?
#18
MartinFXP
closed
4 years ago
1
How to benchmark perturbed ground truth?
#17
MartinFXP
closed
4 years ago
1
Real pathways are incomplete
#16
kpj
closed
4 years ago
1
How to validate (real data) biological results?
#15
kpj
closed
4 years ago
2
Compare multiple performance measurements in benchmarking
#14
kpj
closed
4 years ago
1
Input DAGs may not satisfy faithfulness assumption
#13
kpj
closed
4 years ago
1
How to choose the "correct" link function?
#12
kpj
closed
3 years ago
4
Simulating negative binomial read counts on DAGs
#11
kpj
closed
4 years ago
5
Using causal effects as edge weights can be misleading
#10
kpj
closed
3 years ago
3
How to include library size in the model?
#9
MartinFXP
closed
4 years ago
6
`glm.nb` throws warnings and errors when data is naughty
#8
kpj
closed
4 years ago
3
Helpful links
#7
kpj
closed
4 years ago
1
Why do large networks (>=200 nodes) only produce results when sparse in DCE reconstruction benchmarking?
#6
kpj
closed
4 years ago
1
How to generate synthetic expression profiles
#5
kpj
closed
4 years ago
1
Real pathways are not always DAGs
#4
kpj
closed
4 years ago
1
Understand KEGG pathway structure
#3
kpj
closed
4 years ago
1
How to test for enrichment of a pathway?
#2
MartinFXP
closed
4 years ago
4
How to proceed, if samples in tissue < genes in pathway?
#1
MartinFXP
closed
4 years ago
3