Introduce | Example 1 : Calculating the centrality scores of subpathways. | Example 2 : Calculating the drug-disease reverse association score and corresponding pvalue of drugs. | Visualize 1: Plot a subpathway network structure graph. | Visualize 2: Plot a heatmap of the subpathways that are regulated by disease. | Visualize 3: Plot heatmaps of the subpathways that are regulated by drugs.

Introduction | MAF field requirements | Installation | Overview of the package | Obtain the gene mutation status matrix | Calculate the single-sample mutation-based pathway enrichment score. | Identification of cancer subtypes based on unsupervised spectral clustering algorithm. | Visualization results

Introduction | Example 1: Correlation Plot with Cell Types and Pathways | Example 2: Enrichment Analysis using Multiplex Networks | Example 3: Fit Logistic Regression Model

Introduce | Example 1 : Calculate the GDEscore. | Example 2 : Identify candidate miRNAs by random-walk algorithm. | Example 3 : Build a multivariate Cox regression model using the targets of a single miRNA. | Example 4 : Build a multivariate Cox regression model by integrating the models constructed separately based on different miRNA targets. | Visualize 1: Plot the Kaplan-Meier curve. | Visualize 2: Plot the heatmap of miRNA targets expression. | Visualize 3: Plot the forest diagram. | Visualize 4: Plot the Scatter diagram.

1 Introduce | 2 Example: The inference of the relative abundance matrix of immune cells | 3 Example: Use mutation annotation file (MAF) format data to build a binary mutations matrix | 4 Example: Identification of somatic mutation-driven immune cells. | 5 Example: Visualization

Introduce | Example 1 : Calculate the DEscore. | Example 2 : Calculate drug-drug functional similarity. | Example 3 : Identify candidate drugs by random-walk algorithm. | Visualize 1: Plot the chemical structure of a compound. | Visualize 2: Plot the heatmap of drug targets expression. | Visualize 3: Plot a drug/GO bipartite network.

Introduction | Example 1: Calculate the enrichment scores of drugs. | Example 2. Get the influence of the specific disease in the PPI network | Example 3. Calculate the consistency of the prediction | Multicore capability | Supplementary data files | Known bugs

Introduction | Identifying drug-regulated subpathways | Infer patient-specific subpathway activity profiles. | Calculating drug-disease reverse association score. | Identifying cancer subtype-specific drugs | Calculating the cancer subtype-specific drug score | Estimating statistically significance level of sutype-specific drug score | Visualization | Plot a heat map of normalized drug-disease reverse association scores for cancer samples | Plot heat map of patient-specific subpathway activity profiles of drug-regulated subpathway | Plot a global graph of the drug | Polt a subpathway network graph | Visualize the chemical structure of the drug | References