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DiNAR & SKM

DiNAR (Differential Network Analysis in R) allows for the examination and visualisation of differential (gene) expression within prior knowledge graphs.

To use CKN or PSS as the prior knowledge networks in DiNAR, you can follow the steps here:

  1. Obtain the (sub)network of interest. This can be done by using extracting a subnetwrk yourself (e.g. see the use cases) or downloading the result of a query in the PSS or CKN Explorers. Export nodes and edges as .csv In the case of PSS, the entire network is also visualisable (download from https://skm.nib.si/downloads/pss/public/dinar-edges).

  1. Download and run Custom Network GMM-SKM-KnetMiner app locally or from shinyapps
  2. Load files
  3. Follow instructions and save Custom Network Tables (Nodes/Vertices and Reactions/Edges)
  4. Load Custom Network and Expression Tables into DiNAR
  5. Export results as wished (e.g.)

(*) Take care of empty strings in tables in general, replace them with -

(**) Try to keep shortName short