Package: HiCExperiment 1.7.0

Jacques Serizay

HiCExperiment: Bioconductor class for interacting with Hi-C files in R

R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.

Authors:Jacques Serizay [aut, cre]

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HiCExperiment.pdf |HiCExperiment.html✨
HiCExperiment/json (API)

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

Peer review:

Bug tracker:https://github.com/js2264/hicexperiment/issues

Datasets:
  • centros_yeast - Example datasets provided in 'HiCExperiment' & 'HiContactsData'

On BioConductor:HiCExperiment-1.7.0(bioc 3.21)HiCExperiment-1.6.0(bioc 3.20)

hicdna3dstructuredataimport

6.94 score 9 stars 2 packages 32 scripts 256 downloads 45 exports 66 dependencies

Last updated 24 days agofrom:5db289f951. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winNOTENov 19 2024
R-4.5-linuxNOTENov 19 2024
R-4.4-winNOTENov 19 2024
R-4.4-macNOTENov 19 2024
R-4.3-winNOTENov 19 2024
R-4.3-macNOTENov 19 2024

Exports:AggrHiCExperimentanchorsasas.data.frameas.matrixavailableChromosomesavailableResolutionsbinsciscm2matrixcontacts_yeastcontacts_yeast_eco1CoolFiledf2giexportfileNamefocusfocus<-gi2cmHiCExperimentHicFileHicproFileimportinteractionsinteractions<-makeHiCExperimentFromGInteractionsmetadatametadata<-pairsFilePairsFilepairsFile<-refocusregionsresolutionresolutionsscoresscores<-seqinfoshowslicessubsetByOverlapstopologicalFeaturestopologicalFeatures<-transzoom

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelbitbit64clicodetoolscpp11crayoncurlDelayedArraydplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehmshttrInteractionSetIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigprettyunitsprogressR6Rcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorssnowSparseArraystrawrSummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXVectorzlibbioc

Introduction to HiCExperiment

Jacques Serizay

Rendered fromHiCExperiment.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-01-10
Started: 2022-11-17

Readme and manuals

Help Manual

Help pageTopics
'AggrHiCExperiment' S4 classAggrHiCExperiment AggrHiCExperiment-class show,AggrHiCExperiment-method slices,AggrHiCExperiment,character-method slices,AggrHiCExperiment,missing-method slices,AggrHiCExperiment,numeric-method
Coercing functionsas as.data.frame,HiCExperiment-method as.matrix,HiCExperiment-method cm2matrix coerce,HiCExperiment,ContactMatrix-method coerce,HiCExperiment,data.frame-method coerce,HiCExperiment,GInteractions-method coerce,HiCExperiment,InteractionSet-method coerce,HiCExperiment,matrix-method df2gi gi2cm
HiCExperiment binning methodsbin,GInteractions,character-method bin,GInteractions,numeric-method bin,PairsFile,numeric-method bin-methods
'ContactsFile' S4 classContactsFile ContactsFile-class ContactsFile-methods metadata<-,ContactsFile,list-method metadata<-,ContactsFile-method pairsFile,ContactsFile-method resolution,ContactsFile-method
'CoolFile' S4 classCoolFile CoolFile-class CoolFile-methods McoolFile-class show,CoolFile-method
Example datasets provided in 'HiCExperiment' & 'HiContactsData'centros_yeast contacts_yeast contacts_yeast_eco1 data
HiCExperiment export methodsexport export,HiCExperiment,missing,character-method export-methods
'HiCExperiment' S4 class$,HiCExperiment-method $<-,HiCExperiment-method anchors,HiCExperiment-method bins,HiCExperiment-method cis,HiCExperiment-method fileName,HiCExperiment-method focus,HiCExperiment-method focus<-,HiCExperiment,character-method focus<-,HiCExperiment-method HiCExperiment HiCExperiment-class interactions,HiCExperiment-method interactions<-,HiCExperiment,GInteractions-method interactions<-,HiCExperiment-method length,HiCExperiment-method makeHiCExperimentFromGInteractions metadata<-,HiCExperiment,list-method metadata<-,HiCExperiment-method pairsFile,HiCExperiment-method pairsFile<-,HiCExperiment,character-method pairsFile<-,HiCExperiment-method refocus,HiCExperiment,character-method regions,HiCExperiment-method resolution,HiCExperiment-method resolutions,HiCExperiment-method scores,HiCExperiment,character-method scores,HiCExperiment,missing-method scores,HiCExperiment,numeric-method scores,HiCExperiment-method scores<-,HiCExperiment,character,numeric-method scores<-,HiCExperiment-method seqinfo,HiCExperiment-method show,HiCExperiment-method subsetByOverlaps,HiCExperiment,GInteractions-method subsetByOverlaps,HiCExperiment,GRanges-method subsetByOverlaps,HiCExperiment,logical-method subsetByOverlaps,HiCExperiment,numeric-method subsetByOverlaps,HiCExperiment,Pairs-method topologicalFeatures,HiCExperiment,character-method topologicalFeatures,HiCExperiment,missing-method topologicalFeatures,HiCExperiment,numeric-method topologicalFeatures,HiCExperiment-method topologicalFeatures<-,HiCExperiment,character,GRangesOrGInteractions-method topologicalFeatures<-,HiCExperiment-method trans,HiCExperiment-method zoom,HiCExperiment,numeric-method [,HiCExperiment,character,ANY,ANY-method [,HiCExperiment,GInteractions,ANY,ANY-method [,HiCExperiment,GRanges,ANY,ANY-method [,HiCExperiment,logical,ANY,ANY-method [,HiCExperiment,numeric,ANY,ANY-method [,HiCExperiment,Pairs,ANY,ANY-method [,HiCExperiment-method
'HicFile' S4 classHicFile HicFile-class HicFile-methods show,HicFile-method
'HicproFile' S4 classHicproFile HicproFile-class HicproFile-methods show,HicproFile-method
HiCExperiment import methodsavailableChromosomes,ANY-method availableChromosomes,CoolFile-method availableChromosomes,HicFile-method availableChromosomes,HicproFile-method availableResolutions,ANY-method availableResolutions,CoolFile-method availableResolutions,HicFile-method availableResolutions,HicproFile-method import import,CoolFile,ANY,ANY-method import,CoolFile-method import,HicFile,ANY,ANY-method import,HicFile-method import,HicproFile,ANY,ANY-method import,HicproFile-method import,PairsFile,ANY,ANY-method import,PairsFile-method import-methods
'PairsFile' S4 classPairsFile pairsFile,PairsFile-method PairsFile-class