Licensing | Citing | Introduction | Installation | General workflow | Gene-Term network loadable in Cytoscape | Run an enrichment analysis | Start Cytoscape | Create a gene-term network | Enrichment map | Create an enrichment map in a ggplot format | Using list of term IDs | Enrichment map customization | Create an enrichment map in an igraph format | Effect of seed value | Enrichment map with groups from different enrichment analyses | Create an enrichment map using multiple enrichment analyses in a ggplot format | Create an enrichment map using multiple enrichment analyses in an igraph format | Enrichment map with groups from same enrichment analysis or from complex designs | Create an enrichment map using mutliple subsections of one enrichment analysis in a ggplot format | Create an enrichment map using a complex design | Create an enrichment map using mutliple subsections of one enrichment analysis in a igraph format | Create an enrichment map using mutliple subsections of multiple enrichment analyses in a igraph format | Code Ocean Capsule | Acknowledgments | Session info | References

Licensing and citing | Introduction | The consensusSeekeR package | Loading consensusSeekeR package | Inputs | Positions and Ranges | Chromosomes information | Read NarrowPeak files | Case study: nucleosome positioning | Comparing nucleosome positioning results from different software | Case study: ChIP-Seq data | ChIP-Seq replicates from one experiment | ChIP-Seq data from multiple experiments | Parameters | Effect of the shrinkToFitPeakRegion parameter | Effect of the expandToFitPeakRegion parameter | Effect of the extendingSize parameter | Parallelizing consensusSeekeR | Acknowledgment | Session info | References

Licensing | Citing | Introduction | Installation | Workflow for metrics calculated using CNV status calls | Data Input - Copy number file containing the CNV status calls | Data Importation - GRangesList | Metric Calculation | Metric Visualization | Metrics using the CNV status calls | Sørensen | Szymkiewicz–Simpson | Jaccard | Workflow for metrics calculated using the level of amplification/deletion | Data Input - Copy number file containing the level of amplification/deletion | Metrics using the level of amplification/deletion | Weighted Euclidean Distance-Based | Copy number profile simulating method | Supplementary information | Using parallelization | Creating your own GRangesList | Reproducible research | Acknowledgments | Session info | References

Licensing and citing | Introduction | Loading r Rpackage("nucleoSim") package | Description | Synthetic Nucleosome Maps | Create a nucleosome map using syntheticNucMapFromDist() | Simulate hybridization data of Tiling Arrays | Synthetic Nucleosome Samples | Create a nucleosome sample using syntheticNucReadsFromDist() | Create a nucleosome sample using syntheticNucReadsFromMap() | Session info

Metrics which estimate similarity between two ChIP-Seq profiles | Introduction | Loading the similaRpeak package | Inputs | ChIP-Seq profiles vectors | Metrics | Metric versus Pseudometric | Metrics Presentation | RATIO_AREA | DIFF_POS_MAX | RATIO_MAX_MAX | RATIO_INTERSECT | RATIO_NORMALIZED_INTERSECT | SPEARMAN_CORRELATION | Using similaRpeak on real ChIP-Seq profiles | Metrics calculation using a MetricFactory object | Session info | References

Licensing and citing | Introduction | Loading the RJMCMC package | RJMCMCNucleosomes analysis | RJMCMCNucleosomes analysis step by step | Split the analyzed region into segments | Run RJMCMCNucleosomes for nucleosome predictions | Regroup all regions | Post-process predictions | Visualisation of the predicted nucleosomes | RJMCMCNucleosomes analysis of one chromosome in one step | Session info | References