Citing HiContacts | Basics: importing .(m)/cool files as HiCExperiment objects | Plotting matrices | Plot matrix heatmaps | Plot loops | Plot borders | Plot aggregated matrices over features | Arithmetics | Computing autocorrelated contact map | Detrending contact map (map of scores over expected) | Summing two maps | Computing ratio between two maps | Despeckling (smoothing out) a contact map | Mapping topological features | Chromosome compartments | Diamond insulation score and chromatin domains borders | Contact map analysis | Virtual 4C | Cis-trans ratios | P(s) | Session info
Package: HiContacts 1.15.0
Jacques Serizay
HiContacts: Analysing cool files in R with HiContacts
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
Authors:
HiContacts_1.15.0.tar.gz
HiContacts_1.15.0.zip(r-4.7)HiContacts_1.15.0.zip(r-4.6)HiContacts_1.15.0.zip(r-4.5)
HiContacts_1.15.0.tgz(r-4.6-any)HiContacts_1.15.0.tgz(r-4.5-any)
HiContacts_1.15.0.tar.gz(r-4.7-any)HiContacts_1.15.0.tar.gz(r-4.6-any)
HiContacts_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HiContacts/json (API)
| # Install 'HiContacts' in R: |
| install.packages('HiContacts', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/js2264/hicontacts/issues
On BioConductor:HiContacts-1.15.0(bioc 3.24)HiContacts-1.14.0(bioc 3.23)
Last updated from:b79545c650. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 338 | ||
| linux-devel-x86_64 | OK | 556 | ||
| source / vignettes | OK | 551 | ||
| linux-release-x86_64 | OK | 645 | ||
| macos-release-arm64 | OK | 320 | ||
| macos-oldrel-arm64 | OK | 412 | ||
| windows-devel | OK | 701 | ||
| windows-release | OK | 695 | ||
| windows-oldrel | OK | 716 | ||
| wasm-release | OK | 262 |
Exports:afmhotrColorsaggregateautocorrelatebbrColorsbgrColorsboostbwrColorscisTransRatiocoarsenContactscontacts_yeastcontacts_yeast_eco1coolerColorscoveragedespeckledetrenddistanceLawdividegetBordersgetCompartmentsgetDiamondInsulationgetLoopslocalDistanceLawmergemontagenormalizeplot4CplotMatrixplotPsplotPsSlopeplotSaddleplotScalogramrainbowColorsscalogramsubsamplevirtual4C
Dependencies:abindaskpassbase64encbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelbitbit64Cairoclicliprcodetoolscpp11crayoncurlDelayedArraydir.expirydplyrfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicRangesggbeeswarmggplot2ggrastrgluegtableHiCExperimenthmshttrInteractionSetIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6raggRColorBrewerRcppRcppEigenreadrrhdf5rhdf5filtersRhdf5librlangRSpectraS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystrawrstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviporviridisLitevroomwithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| HiContacts arithmetics functionalities | aggregate,HiCExperiment-method arithmetics autocorrelate boost coarsen despeckle detrend divide merge,HiCExperiment,HiCExperiment-method normalize,HiCExperiment-method subsample |
| cisTransRatio | cisTransRatio |
| Contacts | Contacts |
| Compute the law of distance-dependent contact frequency, a.k.a. P(s) | distanceLaw distanceLaw,GInteractions,missing-method distanceLaw,HiCExperiment,GRanges-method distanceLaw,HiCExperiment,missing-method distanceLaw,PairsFile,GRanges-method distanceLaw,PairsFile,missing-method localDistanceLaw Ps |
| Contact map compartments | getCompartments |
| Contact map insulation | getBorders getDiamondInsulation |
| Finding loops in contact map | getLoops |
| HiContacts plotting functionalities | HiContacts-plots |
| Matrix palettes | afmhotrColors bbrColors bgrColors bwrColors coolerColors palettes rainbowColors |
| Plotting virtual 4C profiles | plot4C |
| Plotting a contact matrix | montage montage,AggrHiCExperiment-method plotMatrix plotMatrix,AggrHiCExperiment-method plotMatrix,GInteractions-method plotMatrix,HiCExperiment-method plotMatrix,matrix-method |
| Plotting a P(s) distance law | plotPs plotPsSlope |
| Plotting saddle plots | plotSaddle |
| Plotting scalograms | plotScalogram |
| Compute a scalogram of contacts | scalogram |
| Aligning tracks with HiCExperiment objects | coverage,HiCExperiment-method tracks |
| Computing virtual 4C profiles | virtual4C |
