Package: HiCool 1.5.0

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_1.5.0.tar.gz
HiCool_1.5.0.zip(r-4.5)HiCool_1.5.0.zip(r-4.4)HiCool_1.5.0.zip(r-4.3)
HiCool_1.5.0.tgz(r-4.4-any)HiCool_1.5.0.tgz(r-4.3-any)
HiCool_1.5.0.tar.gz(r-4.5-noble)HiCool_1.5.0.tar.gz(r-4.4-noble)
HiCool_1.5.0.tgz(r-4.4-emscripten)HiCool_1.5.0.tgz(r-4.3-emscripten)
HiCool.pdf |HiCool.html✨
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-1.5.0(bioc 3.20)HiCool-1.4.0(bioc 3.19)

bioconductor-package

6 exports 0.36 score 122 dependencies

Last updated 2 months agofrom:fda0f1a04f

Exports:getHiCoolArgs getHicStats getLoops HiCool HiCReport importHiCoolFolder

Dependencies:abind askpass base64enc basilisk basilisk.utils BH Biobase BiocGenerics BiocIO BiocParallel bit bit64 bookdown bslib cachem cli codetools colorspace cpp11 crayon crosstalk curl data.table DelayedArray digest dir.expiry dplyr evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plotly png prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp RcppTOML reticulate rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown rmdformats rprojroot S4Arrays S4Vectors sass scales sessioninfo snow SparseArray strawr stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XVector yaml zlibbioc

HiCool

Jacques Serizay

Rendered fromHiCool.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-02-16
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