| compute_perturbation_score | Compute Single Sample Perturbation Score |
| 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 |
| logCPM_example | logCPM_example: Normalised logCPM of patient-derived explant models obtained from 5 ER-positive primamry breast cancer patients (GSE80098) |
| metadata_example | metadata_example: Sample metadata for malignant breast cancer tumors PDE from 5 ER+ breast cancer patients (GSE80098) |
| normalise_by_permu | Normalise test perturbation scores by permutation |
| plot_gs_network | Plot gene-set network |
| retrieve_topology | Retrieve pathway topology as weighted adjacent matrix |
| sSNAPPY | sSNAPPY: A package for testing directional single sample pathway perturbation |
| weight_ss_fc | Compute weighted single sample LogFCs from normalised logCPM |
| weight_ss_fc-method | Compute weighted single sample LogFCs from normalised logCPM |