Package: HiCool 1.13.1

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_1.13.1.tar.gz
HiCool_1.13.1.zip(r-4.7)HiCool_1.13.1.zip(r-4.6)HiCool_1.13.1.zip(r-4.5)
HiCool_1.13.1.tgz(r-4.6-any)HiCool_1.13.1.tgz(r-4.5-any)
HiCool_1.13.1.tar.gz(r-4.7-any)HiCool_1.13.1.tar.gz(r-4.6-any)
HiCool_1.13.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HiCool/json (API)

# Install 'HiCool' in R:

install.packages('HiCool', repos = c('https://bioc.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)

hic dna3dstructure dataimport

4.78 score 2 stars 8 scripts 6 exports 117 dependencies

Last updated from:3cffa64ad0. Checks:1 WARNING, 4 NOTE, 2 OK, 3 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	231
linux-devel-x86_64	NOTE	527
source / vignettes	OK	407
linux-release-x86_64	NOTE	596
macos-release-arm64	NOTE	422
macos-oldrel-arm64	NOTE	318
windows-devel	ERROR	436
windows-release	ERROR	456
windows-oldrel	ERROR	445
wasm-release	OK	207

Exports:getHiCoolArgs getHicStats getLoops HiCool HiCReport importHiCoolFolder

Dependencies:abind askpass base64enc basilisk basilisk.utils BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel bit bit64 bookdown bslib cachem cli codetools cpp11 crayon crosstalk curl data.table DelayedArray digest dir.expiry dplyr evaluate farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gtable here HiCExperiment highr hms htmltools htmlwidgets httr InteractionSet IRanges isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly png prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp RcppTOML reticulate rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown rmdformats rprojroot S4Arrays S4Vectors S7 sass scales Seqinfo sessioninfo snow SparseArray strawr stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite vroom withr xfun XVector yaml

HiCool

Processing sequencing Hi-C libraries with HiCool | Optional parameters | Output files | System dependencies | Session info

Rendered fromHiCool.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Finding loops in contact map	getLoops
Processing Hi-C paired-end fastq files in R	getHiCoolArgs getHicStats HiCool importHiCoolFolder
HiC processing report	HiCReport