Table 1.

Scoring methods offered in FELLA, chosen by the enrich function arguments method and approx

Method	Approx	Notation in [12]	Comment
Hypergeom	N/A	Hypergeometric test	Included for reference
Diffusion	Normality	HD norm	Heat diffusion scores followed by z-scores
Diffusion	Simulation	HD sim	Heat diffusion scores followed by permutations
Pagerank	Normality	PR norm	PageRank scores followed by z-scores
Pagerank	Simulation	PR sim	PageRank scores followed by permutations

Each row corresponds to a method mentioned in the original publication [12]. The method hypergeom is Fisher’s exact test, included for reference. Method diffusion scores the nodes using the heat diffusion model. Method pagerank uses the PageRank algorithm on an upwards-directed version of the network. Both scores undergo a statistical normalisation to remove structural biases, controlled through the approx argument. The user can choose the fast, parametric z-scores (normality) or the slower, non-parametric permutation analysis (simulation). N/A: non-applicable