| generate_permuted_scores | Permute sample labels to simulate null distribution of perturbation scores |
| generate_permuted_scores-method | 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 |
| weight_ss_fc-method | Compute weighted single sample LogFC from normalised logCPM |