Changes in version 1.6.1 - Added drop parameter to path_pert() and generate_permuted_scores() function Changes in version 1.4.4 (2023-10-09) - Remove databases that are no longer supported: pathbank, panther, pharmgkb, smpdb Changes in version 1.4.3 (2023-07-31) - Updated the perturbation scoring step to account for the orientiaton of topology matrices for KEGG pathways (row - Downstream genes; column - Upstream genes) - Add prefix parameter to the weight_ss_fc function to allow user-specified prefix that are other than "ENTREZID:" Changes in version 1.4.2 (2023-07-12) - Updated the permtuation strategy so that the generate_permuted_scores function now construct all possible permuted pairs by default - Updated the plot_community function so KEGG pathways that are not assigned to categories will be ignored in community labeling Changes in version 1.1.0 (2022-06-27) - Fixed a few typos Changes in version 1.0.3 (2022-11-24) - Replaced compute_perturbation_score with raw_gene_pert, path_gene_per and rank_gene_pert to allow the scoring of gene-wise perturbation - Added 3 new visualisation functions: plot_gene_contribution, plot_community and plot_gs2gene - Demonstrated the use of new functions in the updated version of vignette Changes in version 1.0.2 (2022-08-03) - Fixed a missing column name problems in weight_ss_fc Changes in version 0.99.0 (2022-03-28) - Submitted to Bioconductor