Single-Sample Mutation-Based Pathway Analysis
Calculate the single-sample mutation-based pathway enrichment score.
Determining cancer subtypes using unsupervised spectral clustering alg...
Calculate the local wight of seed nodes.
Perform the univariate Cox proportional hazards regression analysis.
Plotting the density ridges plot.
Converts MAF file or data in other formats into mutation matrix.
Plotting the Dot plot.
Calculate the enrichment score of the pathways .
Plotting a heatmap with subtype labels.
Indicator function.
A global propagation algorithm, random walk with restart (RWR), to pre...
Drawing a waterfall plot of a particular pathway.
A systematic bioinformatics tool to perform single-sample mutation-based pathway analysis by integrating somatic mutation data with the Protein-Protein Interaction (PPI) network. In this method, we use local and global weighted strategies to evaluate the effects of network genes from mutations according to the network topology and then calculate the mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. Subsequently, the ssMutPES profiles are used for unsupervised spectral clustering to identify cancer subtypes.