Overview | Importing Interaction Data: load_interactions() | What is a HiCaptuRe object? | Inspecting the HiCaptuRe Object | Tracking Parameters Used in Each Step | Digesting the Genome: digest_genome() | Enzyme Parameters | Controlling Genome Digestion | Performance and Caching | Annotating Interactions: annotate_interactions() | Filtering Interactions | Filtering interactions by Baits of interest: interactionsByBaits() | Bait Summary: getByBaits() | Filtering by Genomic Regions: interactionsByRegions() | Regions Summary: getByRegions() | Intersecting Interaction Sets: intersect_interactions() | Summarizing Interaction Distances: distance_summary | Visualizing Distance Distributions: plot_distance_summary() | Extracting Interactions from a peakmatrix: peakmatrix2list() | Exporting Processed Interaction Data: export_interactions() | SessionInfo
Package: HiCaptuRe 1.3.0
Laureano Tomas-Daza
HiCaptuRe: HiCaptuRe: Manipulating and integrating Capture Hi-C data
Capture Hi-C is a set of techniques that enable the detection of genomic interactions involving regions of interest, known as baits. By focusing on selected loci, these approaches reduce sequencing costs while maintaining high resolution at the level of restriction fragments. HiCaptuRe provides tools to import, annotate, manipulate, and export Capture Hi-C data. The package accounts for the specific structure of bait–otherEnd interactions, facilitates integration with other omics datasets, and enables comparison across samples and conditions.
Authors:
HiCaptuRe_1.3.0.tar.gz
HiCaptuRe_1.3.0.zip(r-4.7)HiCaptuRe_1.3.0.zip(r-4.6)HiCaptuRe_1.3.0.zip(r-4.5)
HiCaptuRe_1.3.0.tgz(r-4.6-any)HiCaptuRe_1.3.0.tgz(r-4.5-any)
HiCaptuRe_1.3.0.tar.gz(r-4.7-any)HiCaptuRe_1.3.0.tar.gz(r-4.6-any)
HiCaptuRe_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HiCaptuRe/json (API)
| # Install 'HiCaptuRe' in R: |
| install.packages('HiCaptuRe', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lauretomas/hicapture/issues
On BioConductor:HiCaptuRe-1.3.0(bioc 3.24)HiCaptuRe-1.2.0(bioc 3.23)
epigeneticshicsequencingdataimportsoftware
Last updated from:5fa64f901d. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 306 | ||
| linux-devel-x86_64 | OK | 634 | ||
| source / vignettes | OK | 453 | ||
| linux-release-x86_64 | OK | 591 | ||
| macos-release-arm64 | OK | 353 | ||
| macos-oldrel-arm64 | OK | 310 | ||
| windows-devel | OK | 459 | ||
| windows-release | OK | 456 | ||
| windows-oldrel | OK | 454 | ||
| wasm-release | OK | 277 |
Exports:annotate_interactionsdigest_genomedistance_summaryexport_interactionsgetByBaitsgetByRegionsgetParametersinteractionsByBaitsinteractionsByRegionsintersect_interactionsload_interactionspeakmatrix2listplot_distance_summary
Dependencies:abindadmiscAnnotationDbiAnnotationFilteraplotaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbootbroomBSgenomebslibcachemcarcarDatacaToolscheckmatecigarillocliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirDerivdichromatdigestdoBydplyrensembldbevaluatefarverfastmapfilelockfontawesomeforcatsforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggfunggplot2ggplotifyggpubrggrepelggsciggsignifggVennDiagramgluegplotsgridExtragridGraphicsgtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpillarpkgconfigplyrpngpolynomprettyunitsprogressProtGenericspurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstatixrstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDatetinytexUCSC.utilsUpSetRurcautf8VariantAnnotationvctrsvennviridisLitewithrxfunXMLxml2XVectoryamlyulab.utilszoo
HiCaptuRe Functions
Last update: 2025-08-11
Started: 2023-12-14
HiCaptuRe Introduction
Installation | Overview | Motivation for Bioconductor | Basic Vocabulary | Data Origin and Experimental Workflow | Capture Hi-C Data Formats (some CHiCAGO outputs) | interBed - ibed — Recommended Format | peakmatrix — Multi-sample Interaction Matrix | seqMonk — Two-row Interaction Format | **bedpe ** — Generic Paired-End Interaction Format | **washU ** — Minimal Format for Browser Upload | **washUold ** — (Legacy) | Summary | The HiCaptuRe Object | Typical Workflow | Example Data | 📚 References | SessionInfo
Last update: 2025-08-11
Started: 2023-12-14
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotates HiCaptuRe object from load_interactions | annotate_interactions |
| Digest genome for a specific restriction enzyme | digest_genome |
| Computes the number of interactions by distance | distance_summary |
| Export interactions in the desired output format | export_interactions |
| Internal functions to access data held in a HiCaptuRe object. | getByBaits getByBaits,HiCaptuRe-method getByRegions getByRegions,HiCaptuRe-method getParameters getParameters,HiCaptuRe-method getters |
| HiCaptuRe Class | HiCaptuRe-class |
| Filters HiCaptuRe object by baits | interactionsByBaits |
| Filters HiCaptuRe object by overlaping regions | interactionsByRegions |
| Computes the intersect between a list of interactions objects | intersect_interactions |
| Loads interaction file into GenomicInteractions Object | load_interactions |
| Creates a list of HiCaptuRe objects based on a peakmatrix | peakmatrix2list |
| Generate the plot based on distance output | plot_distance_summary |
