Package: HiCaptuRe 1.2.0
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_1.2.0.tar.gz
HiCaptuRe_1.2.0.zip(r-4.7)HiCaptuRe_1.2.0.zip(r-4.6)HiCaptuRe_1.2.0.zip(r-4.5)
HiCaptuRe_1.2.0.tgz(r-4.6-any)HiCaptuRe_1.2.0.tgz(r-4.5-any)
HiCaptuRe_1.2.0.tar.gz(r-4.7-any)HiCaptuRe_1.2.0.tar.gz(r-4.6-any)
HiCaptuRe_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HiCaptuRe/json (API)
NEWS
| # Install 'HiCaptuRe' in R: |
| install.packages('HiCaptuRe', repos = c('https://bioc-release.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:8d22eb4164 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 327 | ||
| linux-devel-x86_64 | OK | 623 | ||
| source / vignettes | OK | 489 | ||
| linux-release-x86_64 | OK | 591 | ||
| macos-release-arm64 | OK | 439 | ||
| macos-oldrel-arm64 | OK | 422 | ||
| windows-devel | OK | 871 | ||
| windows-release | OK | 918 | ||
| windows-oldrel | OK | 791 | ||
| wasm-release | OK | 255 |
Exports:annotate_interactionsdigest_genomedistance_summaryexport_interactionsgetByBaitsgetByRegionsgetParametersinteractionsByBaitsinteractionsByRegionsintersect_interactionsload_interactionspeakmatrix2listplot_distance_summary
Dependencies:abindadmiscAnnotationDbiAnnotationFilteraplotaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbootbroomBSgenomebslibcachemcarcarDatacaToolscheckmatecigarillocliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirDerivdichromatdigestdoBydplyrensembldbevaluatefarverfastmapfilelockfontawesomeforcatsforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggfunggplot2ggplotifyggpubrggrepelggsciggsignifggVennDiagramgluegplotsgridExtragridGraphicsgtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpillarpkgconfigplyrpngpolynomprettyunitsprogressProtGenericspurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstatixrstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDatetinytexUCSC.utilsUpSetRurcautf8VariantAnnotationvctrsvennviridisLitewithrxfunXMLxml2XVectoryamlyulab.utilszoo
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 |
