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 |