Overview | Quick start | RGraphSpace attributes | Vertex attributes | Edge attributes | Arrowhead attributes | Passing graphs to geoms | Why camelCase attribute names? | Online tutorials | Other examples | Citation | Session information | References

Context | Package installation and data sets | Inferring evolutionary roots | Evolutionary analysis of regulons generated from breast cancer samples | Mapping root-to-gene annotation | Comparing regulators and targets | Comparing transcription factors and transcription co-factors | Exploring abundance, diversity and plasticity | Evolutionary analysis of regulons generated from normal breast tissue samples | Session information | References

Highlights | Overview | Setting basic input data | Checking graph validity | Creating a PathwaySpace object | Signal projection | Circular projection | Polar projection | Signal types | Online tutorials | Citation | Other useful links | Session information

Overview | Quick start | Initializing the interface | Displaying graphs | Working with containers | Interactive layout | Command-line attributes | Workflow examples | Nested subgraphs | Tree-and-leaf diagrams | Citation | Other useful links | System requirements | Session information

Overview | Quick Start | Package and data requirements | Building a dendrogram example | Converting the hclust object into a tree-and-leaf object | Setting graph attributes | Plotting a tree-and-leaf diagram | Setting the initial tree-and-leaf state with ggtree layouts | Building and plotting a phylo tree with ggtree layouts | Applying tree-and-leaf transformation to ggtree layouts | Case Study 1: visualizing a large dendrogram | Context | Building and plotting a large tree-and-leaf diagram | Case Study 2: visualizing a non-binary tree | Building and plotting a tree-and-leaf for a non-binary tree | Citation | Session information

Overview | Quick Start | Transcriptional Network Inference (TNI) | Transcriptional Network Analysis (TNA) | TCGA-BRCA case study | Context | Package and data requirements | Data preprocessing | Inferring the transcriptional regulatory network | How to select the significance level when inferring regulons from different cohorts | METABRIC case study | Regulon activity profiles | Assessing samples with regulons calculated from a different cohort | Citation | Session information | References

Overview | Quick start | Evolutionary diversity and abundance | Evolutionary rooting | Case studies | High-throughput rooting inference | Map rooting annotation to PPI networks | Map rooting annotation to regulatory networks | Runtime performance of the rooting pipeline | Orthology data packages | Session information | References

Overview | Quick Start | Load datasets | Preprocessing | Run permutation analysis | Run bootstrap analysis | Construct an MBR-class object and apply DPI algorithm | Run association analysis between regulons | Session information | References