Package: linkSet 1.2.0

Gilbert Han

linkSet: Base Classes for Storing Genomic Link Data

Provides a comprehensive framework for representing, analyzing, and visualizing genomic interactions, particularly focusing on gene-enhancer relationships. The package extends the GenomicRanges infrastructure to handle paired genomic regions with specialized methods for chromatin interaction data from Hi-C, Promoter Capture Hi-C (PCHi-C), and single-cell ATAC-seq experiments. Key features include conversion from common interaction formats, annotation of promoters and enhancers, distance-based analyses, interaction strength metrics, statistical modeling using CHiCANE methodology, and tailored visualization tools. The package aims to standardize the representation of genomic interaction data while providing domain-specific functions not available in general genomic interaction packages.

Authors:Gilbert Han [aut, cre]

linkSet_1.2.0.tar.gz
linkSet_1.2.0.zip(r-4.7)linkSet_1.2.0.zip(r-4.6)linkSet_1.2.0.zip(r-4.5)
linkSet_1.2.0.tgz(r-4.6-any)linkSet_1.2.0.tgz(r-4.5-any)
linkSet_1.2.0.tar.gz(r-4.7-any)linkSet_1.2.0.tar.gz(r-4.6-any)
linkSet_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
linkSet/json (API)
NEWS

# Install 'linkSet' in R:
install.packages('linkSet', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gilberthan1011/linkset/issues

Pkgdown/docs site:https://gilberthan1011.github.io

Datasets:

On BioConductor:linkSet-1.3.0(bioc 3.24)linkSet-1.2.0(bioc 3.23)

softwarehicdatarepresentationsequencingsinglecellcoverage

4.78 score 8 scripts 138 downloads 60 exports 104 dependencies

Last updated from:ebca282075 (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR348
linux-devel-x86_64WARNING636
source / vignettesOK520
linux-release-x86_64WARNING593
macos-release-arm64WARNING474
macos-oldrel-arm64WARNING341
windows-develWARNING486
windows-releaseWARNING467
windows-oldrelWARNING498
wasm-releaseOK278

Exports:anchor1anchor1<-anchor2anchor2<-anchorIdsanchorsannotateInterannotatePromoteras.GInteractionsbaitbait<-baitGInteractionsclean_unused_regionscleanUnusedRegionsConvertcountInteractibilitycountInteractionscrossGeneEnhancerdiagnoseLinkSetexportInterBedexportWashUfilterLinksflankflankRegionsgeom_linksetlinkSetnarrownarrowRegionsoeoe<-orderLinkspairdistplot_genomic_rangesplotBaitsplotGenomicRangespromoterRegionspromotersreadvalidPairsreducereduceRegionsregionsregions<-regionsBaitregionsBait<-resizeresizeRegionsrun_chicaneseqinfoshiftRegionsshowshowLinkSetsubsetBaitsubsetBaitRegionsubsetOEthemeLinksetthemeRangetrimunchecked_regions<-widthwithTxDb

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydoParalleldplyrfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrhttr2InteractionSetIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslOrganism.dplyrpatchworkpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Hi-C Workflow with linkSet

Gilbert Han

Rendered fromhic_workthrough.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-07-22
Started: 2024-09-16

linkSet: Base Classes for Storing Genomic Link Data

Gilbert Han

Rendered fromlinkSet.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-07-23
Started: 2024-09-09

Readme and manuals

Help Manual

Help pageTopics
Annotate linkSet with inter/intra chromosome interactionsannotateInter annotateInter,linkSet-method
Annotate the link set with txDb. Give a gene list, and return aannotatePromoter annotatePromoter,linkSet-method
coerce linkSet to DataFrameas.data.frame,linkSet-method
Convert to GInteractionsas.GInteractions as.GInteractions,linkSet-method
linkSet-accessors$ $,linkSet-method $<-,linkSet-method anchor1 anchor1,linkSet-method anchor1<- anchor2 anchor2,linkSet-method anchor2<- anchorIds anchorIds,linkSet-method anchors anchors,linkSet-method bait bait,linkSet-method bait<- bait<-,linkSet-method first first,linkSet-method names names,linkSet-method names<- names<-,linkSet-method oe oe,linkSet-method oe<-,linkSet-method regions regions,linkSet-method regions<- regions<-,linkSet-method regionsBait regionsBait,linkSet-method regionsBait<-,linkSet-method second second,linkSet-method seqinfo seqinfo,linkSet-method unchecked_anchor1 unchecked_anchor1<-,linkSet-method unchecked_anchor2 unchecked_anchor2<-,linkSet-method unchecked_regions unchecked_regions<- unchecked_regions<-,linkSet-method
Convert GInteractions to linkSet with bait annotationsbaitGInteractions baitGInteractions,GInteractions,GRanges,GRanges-method
Character or Missing Class Unioncharacter_Or_missing-class
Clean Unused RegionscleanUnusedRegions cleanUnusedRegions,linkSet-method clean_unused_regions clean_unused_regions,linkSet-method
Convert GInteractions to linkSetConvert Convert,ANY-method Convert,data.frame-method Convert,GInteractions-method Convert,Pairs-method readvalidPairs
Count bait and oe interactibilitycountInteractibility countInteractibility,linkSet-method
Count Bait and Other End InteractionscountBaitOe countInteractions countInteractions,linkSet-method
Cross gene enhancercrossGeneEnhancer crossGeneEnhancer,linkSet-method
Diagnose the linkSet object, return barplot of inter/intra interaction and distance distributiondiagnoseLinkSet diagnoseLinkSet,linkSet-method
Embryo Body BED FileEmbryo_body
Export linkSet to interBed formatexportInterBed exportInterBed,linkSet-method
Export linkSet to WashU browser formatexportWashU exportWashU,linkSet-method
Filter links for further analysisfilterLinks filterLinks,linkSet-method
Add Genome Links to Coverage Plotgeom_linkset geom_linkset,linkSet-method
Example linkSet ObjectlinkExample
linkSet: Base Classes for Storing Genomic Link DatalinkSet
LinkSet objectLinkSet linkSet-class
Create a linkSet object from input datalinkSet,character,GRanges,character_Or_missing-method
Create a linkSet object from input datalinkSet,GRanges,GRanges,character_Or_missing-method
Set Other End (OE) Anchorsoe<-
Order linkSet by mcolsorderLinks orderLinks,linkSet-method
Calculate the distance between bait and the other endpairdist pairdist,linkSet-method
Plot BaitsplotBaits
Plot Genomic RangesplotGenomicRanges plot_genomic_ranges plot_genomic_ranges,linkSet-method
Plot genomic ranges for linkSet objectsplotGenomicRanges,linkSet-method
Reduce Regions in a linkSet ObjectreduceRegions reduceRegions,linkSet-method
Set Bait RegionsregionsBait<-
Run ChICANE Analysisrun_chicane run_chicane,linkSet-method
Display detailed information about a linkSet objectshow,linkSet-method
Show linkSet Object DetailsshowLinkSet showLinkSet,linkSet-method
Subset linkSet object based on bait namessubsetBait subsetBait,linkSet-method subsetBaitRegion subsetBaitRegion,linkSet-method subsetOE subsetOE,linkSet-method
Theme for linkSet plotsthemeLinkset
Theme for genomic range plotsthemeRange
linkSet-GRange-Methodsflank flank,linkSet-method flankRegions flankRegions,linkSet-method narrow narrow,linkSet-method narrowRegions narrowRegions,linkSet-method promoterRegions promoterRegions,linkSet-method promoters promoters,linkSet-method reduce reduce,linkSet-method resize resize,linkSet-method resizeRegions resizeRegions,linkSet-method shift shift,linkSet-method shiftRegions shiftRegions,linkSet-method trim trim,linkSet-method width width,linkSet-method
Database Operation with Connection ManagementwithTxDb withTxDb,character,function-method