Comments (2)
ivanovaos
commented on August 17, 2024
Hi @hmkim,
We are currently working on speeding up and improvements for CARNIVAL. Some things like speeding up of writing constraints are planned to be implemented until the end of the year.
Our lab runs CARNIVAL with cplex. It seems to be quite efficient for the majority of the cases if you run it on cluster. We call runCARNIVAL for each sample. 20 000 genes would be "condensed" to the activity of TFs with DoRothEA/Viper or similar, and you can also make your prior knowledge network smaller by selecting e.g. only edges confirmed by lit references or you can also adapt this network to your specific case. Does this help?
P.S. we have a nice tutorial for the whole pipeline of downstream analysis with CARNIVAL
from carnival.
hmkim
commented on August 17, 2024
@ivanovaos Thank you!
I already checked it (tutorial in your mentioned)
I'll check the cplex on cluster.
from carnival.
Related Issues (20)
- Feature Request: Omnipath network from original paper HOT 2
- Very different results with latest CARNIVAL release HOT 5
- Wrong column name inside the measurementsDf? HOT 1
- cbc error : 'data' must be of a vector type, was 'NULL' despite solution found HOT 1
- Reported 0 for perturbations activity HOT 1
- No DOT figure HOT 1
- Gurobi needs documentation
- How to use CARNIVAL to fit multiple conditions data HOT 2
- Some issues HOT 2
- Failing tests because local files were used HOT 1
- runCARNIVAL HOT 1
- Error in file(file, "rt"): cannot open the connection HOT 2
- progenyMembers.RData HOT 2
- Description about the output HOT 4
- error running Carnival with cbc solver HOT 1
- Carnival usage error HOT 2
- Transcription factors (TFs) absent from final carnival result HOT 12
- [BUG] Your bug or feature request HOT 3
- Using custom network for transcription factor input HOT 11
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