Comments (1)
ptrairatphisan
commented on July 18, 2024
doParallel is for cluster computing and not compulsory.
viper is needed for running DoRothEA. We used to provide a script/pipeline for input data processing in the early versions but not anymore in the latest version.
readr, AnnotationDbi and UniProt.ws are for reading files and mapping between UniprotID and gene symbols in the early versions. This pipeline was also removed in the latest version.
-- Summary: I believe all of these dependencies can be removed. Nevertheless, please recheck whether the CARNIVAL pipeline is still stable after disable/remove these dependencies --
@enio23 @anikaliu - any additional thoughts/comments?
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Related Issues (20)
- Warning message/fix when cplex working folder or output folder are not empty
- Writing cplex command file -> error thrown HOT 23
- 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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