Processing sequencing Hi-C libraries with HiCool | Optional parameters | Output files | System dependencies | Session info

Introduction | Installation | Quick start | Enhanced format support | Comma-separated coordinates | Space-delimited coordinates | Complex chromosome names | Automatic object type detection | Single positions vs. ranges | Genomic interactions | IRanges for non-genomic coordinates | Forcing object types | Working with vectors | Explicit conversion functions | Class detection without parsing | Session Information

Estimating pairs filtering thresholds | Filtering pairs using appropriate thresholds | Computing distance law from pairs | Plotting distance law: first try | Second try: switching to logarithmic scale | Third try: aggregating data before plotting | With some polishing | Reproducibility

Introduction | Installation | CoverageExperiment and AggregatedCoverage classes | CoverageExperiment | AggregatedCoverage | Manipulate CoverageExperiment objects | Create a CoverageExperiment object | Bin a CoverageExperiment object | Expand a CoverageExperiment object | Plot coverage of a set of tracks over a single genomic locus | Manipulate AggregatedCoverage objects | Aggregate a CoverageExperiment into an AggregatedCoverage object | AggregatedCoverage over multiple tracks / feature sets | Plot aggregated coverages with ggplot2 | Use a tidy grammar | Example workflow using tidy grammar | Example use case: AnnotationHub and TxDb resources | Recover TSSs of forward mouse genes | Recover H3K4me3 coverage track from AnnotationHub | Compute the aggregated coverage of H3K4me3 ± 3kb around the TSSs of forward mouse genes | With more genomic tracks | Session info

Stub

OHCA

Introduction to HiContactsData | HiContacts and HiContactsData | Session info

Introduction | Installation | The HiCExperiment class | Basics: importing .(m)cool, .hic or HiC-Pro-generated files as HiCExperiment objects | Import methods | Supporting file classes | Import arguments | Querying subsets of Hi-C matrix files | Multi-resolution Hi-C matrix files | HiCExperiment accessors | Slots | Slot setters | Scores | Features | Coercing HiCExperiment | Importing pairs files | Further documentation | Session info

Introduction | GInteractions objects | Tidy grammar principles | Importing genomic interactions in R | From bed-like text files | From pairs files | Reverting from GInteractions to tabular data frames | Getter functions | anchors | Core GInteractions fields | Metadata columns | Extra genomic-related informations | Pinned (and anchored) GInteractions | PinnedGInteractions | AnchoredPinnedGInteractions | plyranges operations on GInteractions | On PinnedGInteractions objects | On AnchoredPinnedGInteractions objects | dplyr operations on GInteractions | Mutating columns | Grouping columns | Summarizing columns | Filtering columns | Selecting columns | Slicing rows | Overlapping operations on GInteractions | Overlapping GInteractions | Overlapping pinned GInteractions | Citing plyinteractions | Acknowledgments | Reproducibility | Bibliography

Main features of BiocBooks | Creating a BiocBook | The BiocBook class | Editing an existing BiocBook | Publishing an existing BiocBook | Session info

Citing HiContacts | Basics: importing .(m)/cool files as HiCExperiment objects | Plotting matrices | Plot matrix heatmaps | Plot loops | Plot borders | Plot aggregated matrices over features | Arithmetics | Computing autocorrelated contact map | Detrending contact map (map of scores over expected) | Summing two maps | Computing ratio between two maps | Despeckling (smoothing out) a contact map | Mapping topological features | Chromosome compartments | Diamond insulation score and chromatin domains borders | Contact map analysis | Virtual 4C | Cis-trans ratios | P(s) | Session info

Introduction | Installation | HiCExperiment and DNAZooData | Session info

Introduction | Installation | HiCExperiment and fourDNData | Session info

Introduction to periodicDNA | Internal steps of periodicDNA | Quantifying k-mer periodicity over a set of sequences | Basic usage | Repeated shuffling of input sequences | Note | Track of periodicity over a set of Genomic Ranges | Session info