Package: GenomicInteractions 1.41.0
Liz Ing-Simmons
GenomicInteractions: Utilities for handling genomic interaction data
Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.
Authors:
GenomicInteractions_1.41.0.tar.gz
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GenomicInteractions.pdf |GenomicInteractions.html✨
GenomicInteractions/json (API)
NEWS
| # Install 'GenomicInteractions' in R: |
| install.packages('GenomicInteractions', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/computationalregulatorygenomicsicl/genomicinteractions/issues
- hg19.refseq.transcripts - Human Refseq transcripts from chr 17-18
- hic_example_data - Example HiC dataset
- mm9_refseq_promoters - Mouse Refseq promoters from chr 14-15
- thymus_enh - Putative enhancers from mouse thymus data
On BioConductor:GenomicInteractions-1.41.0(bioc 3.21)GenomicInteractions-1.40.0(bioc 3.20)
softwareinfrastructuredataimportdatarepresentationhic
Last updated 24 days agofrom:c7d29047b9. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win | NOTE | Nov 19 2024 |
| R-4.5-linux | NOTE | Nov 19 2024 |
| R-4.4-win | NOTE | Nov 19 2024 |
| R-4.4-mac | NOTE | Nov 19 2024 |
| R-4.3-win | NOTE | Nov 19 2024 |
| R-4.3-mac | NOTE | Nov 19 2024 |
Exports:anchorOneanchorTwoannotateInteractionsannotateRegionsannotationFeaturesasBEDavailableDisplayParscalculateDistancescategoriseInteractionschromosomecountsBetweenAnchorsdescriptiondescription<-endexport.bed12export.bedpeexport.chiasigexport.igraphGenomicInteractionsget_binom_ligation_thresholdget_self_ligation_thresholdinteractionCountsinteractionCounts<-InteractionTrackis.cisis.ddis.dtis.pdis.ppis.ptis.transis.ttisInteractionTypemakeGenomicInteractionsFromFilenamename<-plotAvgViewpointplotCisTransplotCountsplotDistsplotInteractionAnnotationsplotSummaryStatsplotViewpointremoveDupsresetAnnotationsstartsubsetsubsetByFeaturessummariseByFeaturePairssummariseByFeaturesupdateObjectviewPoint
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
Package Vignette for Genomic Interactions: ChIA-PET data
Rendered fromchiapet_vignette.rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2020-04-13
Started: 2014-10-03
HiC vignette for GenomicInteractions package
Rendered fromhic_vignette.Rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2020-04-13
Started: 2014-10-03
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GenomicInteractions | GenomicInteractions-package |
| Function to read in processed Hi-C interaction data generated by hiclib | .importHicLib |
| Function to read in processed Hi-C interaction data generated by HOMER | .importHomer |
| Function to process names relating to interactions stored in bed12 formats. | .processChiapetName |
| Function to read in interaction-data stored in a BAM file | .readBam |
| Function to read in interaction-data stored in a pair of BAM files | .readTwoBams |
| Function to validate tabular input | .validateInput |
| Annotate the interactions in a GInteractions object | annotateInteractions annotateInteractions,GInteractions,list-method |
| Annotate regions | annotateRegions annotateRegions,GInteractions,character,vector-method |
| Coerce to BED structure | asBED,GInteractions-method |
| The default display parameters for a track object class can be queries using the availableDisplayPars function. | availableDisplayPars |
| Calculate interaction distances | calculateDistances calculateDistances,GInteractions-method |
| Get the numbers of interaction types existing in your data | categoriseInteractions |
| Summarise interactions between defined anchors | countsBetweenAnchors countsBetweenAnchors,GInteractions,GRanges-method |
| Export interactions in BED12 format. | export.bed12 export.bed12,GInteractions-method |
| Export interactions in BED Paired-End format. | export.bedpe export.bedpe,GInteractions-method |
| Export interactions in a BEDPE-like format for use with ChiaSig | export.chiasig export.chiasig,GInteractions-method |
| Export interactions to an igraph object. | export.igraph export.igraph,GInteractions-method |
| Function to create a GenomicInteractions object | GenomicInteractions GenomicInteractions,ANY,ANY,ANY-method GenomicInteractions,GInteractions,ANY,ANY-method GenomicInteractions,GInteractions,numeric,ANY-method GenomicInteractions,GRanges,GRanges,GenomicRanges_OR_missing-method GenomicInteractions,GRanges,GRanges,numeric-method GenomicInteractions,missing,missing,GenomicRanges_OR_missing-method GenomicInteractions,numeric,numeric,GRanges-method |
| A S4 class to represent interactions between genomic regions. | GenomicInteractions-class |
| get self ligation threshold with binomial test | get_binom_ligation_threshold |
| Get self ligation threshold with SD method from Heidari et al | get_self_ligation_threshold |
| Functions to access data held in a GenomicInteractions object. | anchorOne anchorOne,GInteractions-method anchorTwo anchorTwo,GInteractions-method annotationFeatures annotationFeatures,GInteractions-method description,GInteractions-method getters interactionCounts interactionCounts,GInteractions-method name name,GInteractions-method |
| Human Refseq transcripts from chr 17-18 | hg19.refseq.transcripts |
| Example HiC dataset | hic_example_data |
| Constructor to create an InteractionTrack object | InteractionTrack |
| A class to hold chromatin interaction data for a specific genomic region | chromosome,InteractionTrack-method end,InteractionTrack-method InteractionTrack-class start,InteractionTrack-method subset,InteractionTrack-method |
| Interaction Type Helpers | InteractionHelpers is.cis is.cis,GInteractions-method is.dd is.dd,GInteractions-method is.dt is.dt,GInteractions-method is.pd is.pd,GInteractions-method is.pp is.pp,GInteractions-method is.pt is.pt,GInteractions-method is.trans is.trans,GInteractions-method is.tt is.tt,GInteractions-method isInteractionType isInteractionType,GInteractions-method |
| Function to create GenomicInteraction objects from a file | makeGenomicInteractionsFromFile |
| Mouse Refseq promoters from chr 14-15 | mm9_refseq_promoters |
| Plot coverage around a set of virtual 4C viewpoints | plotAvgViewpoint |
| Plots the percentages of cis and trans interactions for a GInteractions object as a donut plot. | plotCisTrans |
| Plot a bar chart of the number of interactions supported by different numbers of reads in your data. | plotCounts |
| Plots a histogram of interaction distances for a GInteractions Object | plotDists |
| Plot a donut plot of interaction types for an annotated GInteractions object | plotInteractionAnnotations |
| Plot summary statistics for a GInteractions object | plotSummaryStats |
| Plot coverage around a virtual 4C viewpoint | plotViewpoint |
| Remove all but one occurences of a duplicated interaction | removeDups |
| Reset annotations made to a GInteractions object | resetAnnotations resetAnnotations,GInteractions-method |
| Tests whether anchors have the same strand. | sameStrand |
| Functions to set data held in a GInteractions object. | description<-,GInteractions,ANY-method interactionCounts<- interactionCounts<-,GInteractions-method name<- name<-,GInteractions-method setters |
| Subset a GInteractions object by features | subsetByFeatures subsetByFeatures,GInteractions,character,character-method subsetByFeatures,GInteractions,GRanges,missing-method subsetByFeatures,GInteractions,GRangesList,missing-method |
| Return the total number of interactions in a GInteractions GIObject | sum,GInteractions-method |
| Summarise the number of interactions between two sets of features. | summariseByFeaturePairs summariseByFeaturePairs,GInteractions-method |
| Summary statistics of interactions for a given feature set | summariseByFeatures summariseByFeatures,GInteractions-method |
| Putative enhancers from mouse thymus data | thymus_enh |
| updateObject method for GenomicInteractions 1.3.7 and earlier | updateObject,GenomicInteractions-method |
| Virtual 4C viewpoint | viewPoint |
