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 patients (GSE80098) |
metadata_example |
metadata_example: Sample metadata for malignant breast cancer tumours PDE from 5 ER+ breast cancer patients (GSE80098) |
normalise_by_permu |
Normalise test perturbation scores by permutation results |
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 specific pathway's perturbation as heatmap |
plot_gs2gene |
Plot pathways and genes contained in them as a network |
plot_gs_network |
Plot significantly perturbed gene-sets as a network |
rank_gene_pert |
Rank genes by perturbation scores within each sample |
raw_gene_pert |
Compute Gene-wise Perturbation Score |
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 |