Introduction - What is this package? | Methods - The Model | Work Flow | Loading Data | Quick Start | Step 1 - Extracting Normalised ChIP scores from ChIP-seq datasets | Step 2 - Computing a PWMs | Step 3 - Computing Optimal Parameters | Step 4 - Extracting Optimal Paramters (Prelim) | Step 5 - Plotting Optimal Set of Parameters | Step 6 - Extracting Optimal Set of Parameters with associated data | Step 7 - Plotting ChIP_seq like profiles | Advanced Work | Step 1 - Parameter Set Up | Step 2 - Extracting Normalised ChIP scores. | Step 3 - Position Weight Matrix and Associated Paramters | Step 4 - Computing Optimal Set of Parameters | Step 5 - Extracting and Plotting Optimal Parameters | Step 6 - Computing individual parameter combinations | Step 7 - Plotting Single combination | Parameter Description | Session Info | References

Introduction - What is this package? | Methods - The Chromatin State Model | Using ChIPanalyser | Loading data | ChIPanalyser | External Data | Input data : What is it? | Setting Parameters | Initializing ChIPanalyser | Building Initial objects | Generating a starting population | Pre-processing ChIP data | Evolution | Fitest of them all | Get fitest individual | Running ChIPanalyser with fitest individual | Plotting