Introduction | How to use HiCcompare | Installation | Getting Hi-C Data | Extracting data from .hic files | Extracting data from .cool files | Using data from HiC-Pro | Detecting Copy Number Variations and Excluding regions | Creating the hic.table object | Sparse upper triangular format | BEDPE format | HiC-Pro format | InteractionSet/GRanges format | Total Sum Scaling | Joint Normalization | Difference Detection | Converting HiCcompare results to InteractionSet objects | Simulating Hi-C Data | Additional Functions | Using HiCcompare on a cluster | Session Info

Installation | Introduction | Performing gene ontology analysis using TADCompare | Session Info

Introduction | Getting Started | Installation | Input data | Working with $n \times n$ matrices | Working with $n \times (n+3)$ matrices | Working with sparse 3-column matrices | Working with other data types | Working with .hic files | Working with .cool files | Working with HiC-Pro files | Running SpectralTAD | Filtering TADs | Silhouette score filtering | Z-score filtering | Finding hierarchical TADS | Removing gaps | Running SpectralTAD with parallelization | Effect of matrix type on runtime | Effect of parameters on runtime | Using SpectralTAD output with HiCExplorer and Juicebox | Using SpectralTAD with HiCExplorer | Using SpectralTAD with Juicebox | References

Introduction | Input data | preciseTAD functionality and output | Getting Started | Installation | Implementation | Model building | Construction of the data matrix | Feature selection using recursive feature elimination | Implementing a random forest for boundary prediction | Precise boundary prediction | Running preciseTAD | Using preciseTAD with Juicebox | Cross-cell-type prediction | References

Introduction | Getting Started | Installation | Reading in a file stored on ExperimentHub | Use the pre-trained model to predict TAD boundaries on the holdout chromosome (CHR22) for GM12878 between coordinates 18000000-19000000 at base-level resolution

Introduction | Getting started | Example

Introduction | How to use multiHiCcompare | Install multiHiCcompare from Bioconductor | Getting Hi-C Data | Extracting data from .hic files | Extracting data from .cool files | Using data from HiC-Pro | Parallel Processing | Creating the hicexp object | Sparse upper triangular format | The hicexp object | Normalization | Library scaling | Cyclic Loess Normalization | Fast Loess Normalization (Fastlo) | Difference Detection | Exact Test | GLM Methods | Downstream analysis | Other functions | Session Info

Introduction | Getting Started | Installation | Working with different types of data | Working with $n \times n$ matrices | Working with $n \times (n+3)$ matrices | Working with sparse 3-column matrices | Working with other data types | Working with .hic files | Working with .cool files | Working with HiC-Pro files | Effect of matrix type on runtime | Session Info | References

Installation | TADCompare | Introduction | Running TADcompare | Types of TADCompare output | Pre-specification of TADs | Visualization of TADCompare Results | Comparing TAD boundary scores | Comparing pre-defined TAD boundaries | TimeCompare | Running TimeCompare | ConsensusTAD | Running ConsensusTADs | Session Info | References