This project wants to allow the user to calculate functional similarities (or biological correlation as it was named originally hence the name) and use them for network building or other purposes.
It is an R package you can install it from the Bioconductor project with:
You can install this version of BioCor with:
# The data must be provided, see the vignette for more details. # Get some pathways from the pathway data (pathways <- sample(unlist(genesReact, use.names = FALSE), 5)) #>  "R-HSA-1483255" "R-HSA-6806667" "R-HSA-597592" "R-HSA-977443" #>  "R-HSA-1852241" # Calculate the pathway similarity of them mpathSim(pathways, genesReact, NULL) #> R-HSA-1483255 R-HSA-6806667 R-HSA-597592 R-HSA-977443 #> R-HSA-1483255 1.000000000 0.00000000 0.007952286 0 #> R-HSA-6806667 0.000000000 1.00000000 0.009510870 0 #> R-HSA-597592 0.007952286 0.00951087 1.000000000 0 #> R-HSA-977443 0.000000000 0.00000000 0.000000000 1 #> R-HSA-1852241 0.005291005 0.00000000 0.047702152 0 #> R-HSA-1852241 #> R-HSA-1483255 0.005291005 #> R-HSA-6806667 0.000000000 #> R-HSA-597592 0.047702152 #> R-HSA-977443 0.000000000 #> R-HSA-1852241 1.000000000
It is intended for bioinformaticians, both people interested in knowing the functionally similarity of some genes or clusters and people developing some other analysis at the top of it.
The goal of this project is to provide methods to calculate functional similarities based on pathways.
Here is a non-comprehensive list:
See the advanced vignette
Please read how to contribute for details on the code of conduct, and the process for submitting pull requests.