Package: HiCool 1.12.0

Jacques Serizay

HiCool: HiCool

HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.

Authors:Jacques Serizay [aut, cre]

HiCool_1.12.0.tar.gz
HiCool_1.12.0.zip(r-4.7)HiCool_1.12.0.zip(r-4.6)HiCool_1.12.0.zip(r-4.5)
HiCool_1.12.0.tgz(r-4.6-any)HiCool_1.12.0.tgz(r-4.5-any)
HiCool_1.12.0.tar.gz(r-4.7-any)HiCool_1.12.0.tar.gz(r-4.6-any)
HiCool_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HiCool/json (API)

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

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

On BioConductor:HiCool-1.13.1(bioc 3.24)HiCool-1.12.0(bioc 3.23)

hicdna3dstructuredataimport

4.70 score 2 stars 7 scripts 242 downloads 6 exports 116 dependencies

Last updated from:60d11125d6 (on RELEASE_3_23). Checks:1 WARNING, 4 NOTE, 2 OK, 3 ERROR. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING241
linux-devel-x86_64NOTE528
source / vignettesOK395
linux-release-x86_64NOTE516
macos-release-arm64NOTE495
macos-oldrel-arm64NOTE338
windows-develERROR408
windows-releaseERROR443
windows-oldrelERROR417
wasm-releaseOK186

Exports:getHiCoolArgsgetHicStatsgetLoopsHiCoolHiCReportimportHiCoolFolder

Dependencies:abindaskpassbase64encbasiliskbasilisk.utilsBHBiobaseBiocGenericsBiocIObiocmakeBiocParallelbitbit64bookdownbslibcachemclicodetoolscpp11crayoncrosstalkcurldata.tableDelayedArraydigestdir.expirydplyrevaluatefarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehereHiCExperimenthighrhmshtmltoolshtmlwidgetshttrInteractionSetIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigplotlypngprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppTOMLreticulaterhdf5rhdf5filtersRhdf5librlangrmarkdownrmdformatsrprojrootS4ArraysS4VectorsS7sassscalesSeqinfosessioninfosnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunXVectoryaml

HiCool

Jacques Serizay

Rendered fromHiCool.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2025-07-15
Started: 2023-01-30

Readme and manuals

Help Manual

Help pageTopics
Finding loops in contact mapgetLoops
Processing Hi-C paired-end fastq files in RgetHiCoolArgs getHicStats HiCool importHiCoolFolder
HiC processing reportHiCReport