Comments (6)
Maybe you can check this tutorial here: https://github.com/saezlab/transcriptutorial.
The current version of the vignette is limited in the description because a)The functionalities of the progeny and dorothea packages were not available in Bioconductor yet at the time when CARNIVAL package was submitted in Bioc; and b)Vignette example should be small case studies which should be solved within a limited amount of time. Also while using CARNIVAL we strongly recommend in obtaining a CPLEX license (there's a free academic edition) for solving the CARNIVAL problems rather than the default solver (lpSolve) since the latter is only implemented to pass the necessary Bioconductor tests and can only handle small case-studies before running into memory issues.
The vignettes should be updated in the next CARNIVAL updates in Bioconductor but until then hope the tutorial I have shared to be of help to you.
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Hello,
have you checked this tutorial here ? https://github.com/saezlab/CARNIVAL/blob/master/vignettes/CARNIVAL-vignette.pdf
If so do you mean you don't know how to run dorothea and progeny only ?
Cheers
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So little update:
I've the output of Dorothea -> a matrix that is pathways x patients.
However to use a weight object as input of CARNIVAL, I need weights on nodes of the network that are genes and not pathways. How can I have an output of DOROTHEA useful for CARNIVAL?
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@michelegentili93 let's try to figure it out together.
I've the output of Dorothea -> a matrix that is pathways x patients.
The output of DoRoThEA is a list of TFs, that can be combined with running e.g. VIPER to estimate TF activities. Progeny should generate a list of pathways activities. Do you mean here the output of Progeny then?
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Good day.
After skimming through many hundred commits, it seems the tutorial got truncated multiple times until the vignette looks like it does now. With the real life examples gone, there are only 2 binary small examples with little resemblance to real life data. For a first time user this makes it close to impossible to get the 'raw RNAseq counts' -> 'Carnival input' step right. Is there a new detailed real-life example in the making?
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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
- General Recommendations for preprocessing RNA-Seq data HOT 2
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