Package: HiCExperiment 1.13.0

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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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HiCExperiment/json (API)

# Install 'HiCExperiment' in R:

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

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

Datasets:

centros_yeast - Example datasets provided in 'HiCExperiment' & 'HiContactsData'

On BioConductor:HiCExperiment-1.13.0(bioc 3.24)HiCExperiment-1.12.0(bioc 3.23)

hic dna3dstructure dataimport

7.55 score 13 stars 3 packages 40 scripts 45 exports 59 dependencies

Last updated from:ec0ab688e0. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	211
linux-devel-x86_64	NOTE	580
source / vignettes	OK	419
linux-release-x86_64	NOTE	657
macos-release-arm64	NOTE	342
macos-oldrel-arm64	NOTE	518
windows-devel	NOTE	648
windows-release	NOTE	617
windows-oldrel	NOTE	664
wasm-release	OK	212

Exports:AggrHiCExperiment anchors as as.data.frame as.matrix availableChromosomes availableResolutions bins cis cm2matrix contacts_yeast contacts_yeast_eco1 CoolFile df2gi export fileName focus focus<-gi2cm HiCExperiment HicFile HicproFile import interactions interactions<-makeHiCExperimentFromGInteractions metadata metadata<-pairsFile PairsFile pairsFile<-refocus regions resolution resolutions scores scores<-seqinfo show slices subsetByOverlaps topologicalFeatures topologicalFeatures<-trans zoom

Dependencies:abind BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel bit bit64 cli codetools cpp11 crayon DelayedArray dir.expiry dplyr filelock formatR futile.logger futile.options generics GenomicRanges glue hms InteractionSet IRanges lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats pillar pkgconfig prettyunits progress R6 Rcpp rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors Seqinfo snow SparseArray strawr SummarizedExperiment tibble tidyselect tzdb utf8 vctrs vroom withr XVector

Introduction to HiCExperiment

Rendered fromHiCExperiment.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'AggrHiCExperiment' S4 class	AggrHiCExperiment AggrHiCExperiment-class show,AggrHiCExperiment-method slices,AggrHiCExperiment,character-method slices,AggrHiCExperiment,missing-method slices,AggrHiCExperiment,numeric-method
Coercing functions	as 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 methods	bin,GInteractions,character-method bin,GInteractions,numeric-method bin,PairsFile,numeric-method bin-methods
'ContactsFile' S4 class	ContactsFile ContactsFile-class ContactsFile-methods metadata<-,ContactsFile,list-method metadata<-,ContactsFile-method pairsFile,ContactsFile-method resolution,ContactsFile-method
'CoolFile' S4 class	CoolFile 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 methods	export 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 class	HicFile HicFile-class HicFile-methods show,HicFile-method
'HicproFile' S4 class	HicproFile HicproFile-class HicproFile-methods show,HicproFile-method
HiCExperiment import methods	availableChromosomes,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 class	PairsFile pairsFile,PairsFile-method PairsFile-class