Package: HiContacts 1.9.0
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_1.9.0.tar.gz
HiContacts_1.9.0.zip(r-4.5)HiContacts_1.9.0.zip(r-4.4)HiContacts_1.9.0.zip(r-4.3)
HiContacts_1.9.0.tgz(r-4.4-any)HiContacts_1.9.0.tgz(r-4.3-any)
HiContacts_1.9.0.tar.gz(r-4.5-noble)HiContacts_1.9.0.tar.gz(r-4.4-noble)
HiContacts_1.9.0.tgz(r-4.4-emscripten)HiContacts_1.9.0.tgz(r-4.3-emscripten)
HiContacts.pdf |HiContacts.html✨
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-1.9.0(bioc 3.21)HiContacts-1.8.0(bioc 3.20)
Last updated 2 months agofrom:8328e67219. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | OK | Nov 29 2024 |
| R-4.5-linux | OK | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:afmhotrColorsaggregateautocorrelatebbrColorsbgrColorsboostbwrColorscisTransRatiocoarsenContactscontacts_yeastcontacts_yeast_eco1coolerColorscoveragedespeckledetrenddistanceLawdividegetBordersgetCompartmentsgetDiamondInsulationgetLoopslocalDistanceLawmergemontagenormalizeplot4CplotMatrixplotPsplotPsSlopeplotSaddleplotScalogramrainbowColorsscalogramsubsamplevirtual4C
Dependencies:abindaskpassbeeswarmBHBiobaseBiocGenericsBiocIOBiocParallelbitbit64Cairoclicliprcodetoolscolorspacecpp11crayoncurlDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrgluegtableHiCExperimenthmshttrInteractionSetIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6raggRColorBrewerRcppRcppEigenreadrrhdf5rhdf5filtersRhdf5librlangRSpectraS4ArraysS4VectorsscalessnowSparseArraystrawrstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviporviridisLitevroomwithrXVectorzlibbioc
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 |
