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I intend to use the R codes in http://compbio.cs.toronto.edu/SNF/SNF/Software.html but don't know where to start as all the scripts are function codes. Their page also includes data samples. Is there any direction for applying these codes in R and using one of the five datasets listed in this page? I've already installed the SNFtool package. Thanks.

Sana
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The package used to be available on CRAN. It is now archived, which means you have to go through a few more hoops to install it. See this answer on SO for the process of installing an archived package. Make sure to use the download link for SNFtool instead of the one used in that post. The URL of the most recent version of the package is:

"https://cran.r-project.org/src/contrib/Archive/SNFtool/SNFtool_2.3.0.tar.gz"

Some of the functionality of the package will most likely not work, as the package depends on another package that has been archived in the first place. It might be worthwhile to see if there are alternative packages available to perform the tasks you are interested in, that are not archived and being actively developed.

Till
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  • Thanks Till, I installed SNFtool using the instruction you shared. Would you please let me know what the next step would be and how I could run the R codes directed in http://compbio.cs.toronto.edu/SNF/SNF/Software.html ? – Sana Apr 28 '21 at 19:52