| Cascade-package | The Cascade Package: Selection, Reverse-Engineering and Prediction in Cascade Networks | 
| analyze_network | Analysing the network | 
| analyze_network-method | Analysing the network | 
| analyze_network-methods | Analysing the network | 
| as.micro_array | Coerce a matrix into a micro_array object. | 
| Cascade | The Cascade Package: Selection, Reverse-Engineering and Prediction in Cascade Networks | 
| compare | Some basic criteria of comparison between actual and inferred network. | 
| compare-method | Some basic criteria of comparison between actual and inferred network. | 
| compare-methods | Some basic criteria of comparison between actual and inferred network. | 
| cutoff | Choose the best cutoff | 
| cutoff-method | Choose the best cutoff | 
| cutoff-methods | Choose the best cutoff | 
| dim | Dimension of the data | 
| dim-method | Dimension of the data | 
| dim-methods | Dimension of the data | 
| evolution | See the evolution of the network with change of cutoff | 
| evolution-method | See the evolution of the network with change of cutoff | 
| evolution-methods | See the evolution of the network with change of cutoff | 
| geneNeighborhood | Find the neighborhood of a set of nodes. | 
| geneNeighborhood-method | Find the neighborhood of a set of nodes. | 
| geneNeighborhood-methods | Find the neighborhood of a set of nodes. | 
| genePeakSelection | Methods for selecting genes | 
| genePeakSelection-method | Methods for selecting genes | 
| genePeakSelection-methods | Methods for selecting genes | 
| geneSelection | Methods for selecting genes | 
| geneSelection-method | Methods for selecting genes | 
| geneSelection-methods | Methods for selecting genes | 
| gene_expr_simulation | Simulates microarray data based on a given network. | 
| gene_expr_simulation-method | Simulates microarray data based on a given network. | 
| gene_expr_simulation-methods | Simulates microarray data based on a given network. | 
| head-method | Overview of a micro_array object | 
| head-methods | Overview of a micro_array object | 
| inference | Reverse-engineer the network | 
| inference-method | Reverse-engineer the network | 
| inference-methods | Reverse-engineer the network | 
| M | Simulated M data for examples. | 
| methods | Overview of a micro_array object | 
| micropredict-class | Class '"micropredict"' | 
| micro_array-class | Class '"micro_array"' | 
| Net | Simulated network data for examples. | 
| network | A network object data. | 
| network-class | Class '"network"' | 
| network_random | Generates a network. | 
| Net_inf | Reverse-engineered network of the simulated data. | 
| plot-method | Plot | 
| plot-methods | Plot | 
| position | Returns the position of edges in the network | 
| position-method | Returns the position of edges in the network | 
| position-methods | Returns the position of edges in the network | 
| predict | Prediction of the gene expressions after a knock-out experience 'predict' | 
| predict-method | Prediction of the gene expressions after a knock-out experience 'predict' | 
| predict-methods | Prediction of the gene expressions after a knock-out experience 'predict' | 
| print-method | Methods for Function 'print' | 
| print-methods | Methods for Function 'print' | 
| Selection | Selection of genes. | 
| summary-method | Methods for Function 'summary' | 
| summary-methods | Methods for Function 'summary' | 
| unionMicro | Makes the union between two micro_array objects. | 
| unionMicro-method | Makes the union between two micro_array objects. | 
| unionMicro-methods | Makes the union between two micro_array objects. |