Regarding of CARNIVAL installing

[hmkim]

Hi,

Thank you for the awesome tutorial.

Please write this in the md file.

BiocManager::install("CARNIVAL")

https://github.com/saezlab/transcriptutorial/blob/master/INSTALL.md

[hmkim]

Please write the installing of ILP solvers.

(Refer to this: https://bioconductor.org/packages/release/bioc/vignettes/CARNIVAL/inst/doc/CARNIVAL.html)

In my case, I choose the Cbc in my ubuntu system.

apt install coinor-cbc

and then modified the script.

"scripts/05_network_reconstruction_with_CARNIVAL.md"

# run carnival
carnival_result = runCARNIVAL( inputObj= iniciators,
                               measObj = tfList$t, 
                               netObj = sif, 
                               weightObj = progenylist$score, 
                               solverPath = "/usr/bin/cbc", 
                               solver = "cbc",
                               timelimit=7200,
                               mipGAP=0,
                               poolrelGAP=0 )

[hmkim]

In this script "06_analysis_CARNIVAL_results.Rmd"

Check the path in your case.

setwd("/Users/rosherbal/Projects/transcriptutorial/scripts")

[hmkim]

In this script "06_analysis_CARNIVAL_results.Rmd"

../../Hepatoblastoma-iPC/proteomics/data/c2.cp.v7.1.symbols.gmt

I got this file from here.

https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.1/c2.cp.v7.1.symbols.gmt

[jperales]

@hmkim , thank you very much for your comments! @rosherbal will include the rest and close the issue when finished. Let me know if I could help with anything else.

Javier

[rosherbal]

@hmkim , thanks for your comments. I have added the information about the ILPs. For the pathway analysis, it was already included in the description pointing to MSigDB.

Rosa