Installing the RESOLVE R package | Changelog | Using the RESOLVE R package | Signatures-based clustering and associations to signatures exposures | Current R Session

Overview | Installing SIMLR | Debug

Changelog | Algorithms and useful links | External links to resources related to TRONCO

Modifying events and samples | Modifying patterns | Subsetting a dataset

Summary report for a dataset and boolean queries | Creating views with the as functions | Dataset size | Oncoprints | Groups visualization (e.g., pathways)

Preliminaries | Mutations annotated in a MAF format | Copy Number Variants annotated in the GISTIC format | Custom alterations annotated in a boolean matrix | Downloading data from the cBio portal for cancer genomics

Data consolidation. | CAPRI | Testable hypotheses via logical formulas (i.e., patterns) | Adding custom hypotheses. | Adding (automatically) hypotheses for homologous events. | Adding (automatically) hypotheses for a group of genes. | Querying, visualizing and manipulating CAPRI's patterns. | How to build a pattern. | Model reconstruction | CAPRESE | Directed Minimum Spanning Tree with Mutual Information | Partially Directed Minimum Spanning Tree with Mutual Information | Undirected Minimum Spanning Tree with Likelihood-Fit | Undirected Minimum Spanning Tree with Mutual Information

Visualizing a reconstructed model | Accessing information within a model (e.g., confidence) | Model structure | Empirical probabilities | Confidence measures | Confidence via non-parametric and statistical bootstrap | Confidence via cross-validation (entropy loss, prediction and posterior classification errors)

Overview | Installing OncoScore | Debug

Changelog | Algorithms and useful links