generate_permuted_scores
                        Permute sample labels to simulate null
                        distribution of perturbation scores
gsAnnotation_df         gsAnnotation_df: Categorization of KEGG
                        pathways used for community annotation
logCPM_example          logCPM_example: Normalised logCPM of
                        patient-derived explant models obtained from 5
                        ER-positive primamry breast cancer tumours
                        (GSE80098)
metadata_example        metadata_example: Sample metadata for malignant
                        breast cancer tumours PDE from 5 ER+ breast
                        cancer tumour (GSE80098)
normalise_by_permu      Normalise test perturbation scores by
                        permutation result and compute permutation
                        p-values
pathway_pert            Compute Single-sample Pathway-level
                        Perturbation Score
plot_community          Visualise the community structure in
                        significantly perturbed gene-set network
plot_gene_contribution
                        Plot genes' contribution to a pathway's
                        perturbation as a heatmap
plot_gs2gene            Plot pathways and genes contained in them as a
                        network
plot_gs_network         Plot significantly perturbed gene-sets as a
                        network
raw_gene_pert           Compute Gene-wise Perturbation Score
retrieve_topology       Retrieve pathway topology as weighted adjacency
                        matrices
sSNAPPY                 sSNAPPY: A package for testing directional
                        single sample pathway perturbation
weight_ss_fc            Compute weighted single sample LogFC from
                        normalised logCPM
