Package: HiCool 1.7.1
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:
HiCool_1.7.1.tar.gz
HiCool_1.7.1.zip(r-4.5)HiCool_1.7.1.zip(r-4.4)HiCool_1.7.1.zip(r-4.3)
HiCool_1.7.1.tgz(r-4.5-any)HiCool_1.7.1.tgz(r-4.4-any)HiCool_1.7.1.tgz(r-4.3-any)
HiCool_1.7.1.tar.gz(r-4.5-noble)HiCool_1.7.1.tar.gz(r-4.4-noble)
HiCool_1.7.1.tgz(r-4.4-emscripten)HiCool_1.7.1.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-1.7.0(bioc 3.21)HiCool-1.6.0(bioc 3.20)
Last updated 9 days agofrom:b69d4949ef. Checks:1 OK, 2 NOTE, 6 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 19 2025 |
| R-4.5-win | ERROR | Mar 19 2025 |
| R-4.5-mac | ERROR | Mar 19 2025 |
| R-4.5-linux | NOTE | Mar 19 2025 |
| R-4.4-win | ERROR | Mar 19 2025 |
| R-4.4-mac | ERROR | Mar 19 2025 |
| R-4.4-linux | NOTE | Mar 19 2025 |
| R-4.3-win | ERROR | Mar 19 2025 |
| R-4.3-mac | ERROR | Mar 19 2025 |
Exports:getHiCoolArgsgetHicStatsgetLoopsHiCoolHiCReportimportHiCoolFolder
Dependencies:abindaskpassbase64encbasiliskbasilisk.utilsBHBiobaseBiocGenericsBiocIOBiocParallelbitbit64bookdownbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdir.expirydplyrevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehereHiCExperimenthighrhmshtmltoolshtmlwidgetshttrInteractionSetIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypngprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppTOMLreticulaterhdf5rhdf5filtersRhdf5librlangrmarkdownrmdformatsrprojrootS4ArraysS4VectorssassscalessessioninfosnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXVectoryaml
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 |
