Package: HiContacts 1.15.3

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:Jacques Serizay [aut, cre]

HiContacts_1.15.3.tar.gz
HiContacts_1.15.3.zip(r-4.7-any)HiContacts_1.15.3.zip(r-4.6-any)HiContacts_1.15.3.zip(r-4.5-any)
HiContacts_1.15.3.tgz(r-4.6-any)HiContacts_1.15.3.tgz(r-4.5-any)
HiContacts_1.15.3.tar.gz(r-4.7-any)HiContacts_1.15.3.tar.gz(r-4.6-any)
HiContacts_1.15.3.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-1.15.3(bioc 3.24)HiContacts-1.14.0(bioc 3.23)

hicdna3dstructure

6.33 score 16 stars 1 packages 90 scripts 599 downloads 36 exports 96 dependencies

Last updated from:dfb588e11e. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING210
linux-develERROR510
source / vignettesERROR312
linux-releaseERROR476
macos-releaseERROR325
macos-oldrelERROR362
windows-develERROR421
windows-releaseERROR417
windows-oldrelERROR409
wasm-releaseOK183

Exports:afmhotrColorsaggregateautocorrelatebbrColorsbgrColorsboostbwrColorscisTransRatiocoarsenContactscontacts_yeastcontacts_yeast_eco1coolerColorscoveragedespeckledetrenddistanceLawdividegetBordersgetCompartmentsgetDiamondInsulationgetLoopslocalDistanceLawmergemontagenormalizeplot4CplotMatrixplotPsplotPsSlopeplotSaddleplotScalogramrainbowColorsscalogramsubsamplevirtual4C

Dependencies:abindaskpassbase64encbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelbitbit64Cairoclicliprcodetoolscpp11crayoncurlDelayedArraydir.expirydplyrfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicRangesggbeeswarmggplot2ggrastrgluegtableHiCExperimenthmshttrInteractionSetIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6raggRColorBrewerRcppRcppEigenreadrrhdf5rhdf5filtersRhdf5librlangRSpectraS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystrawrstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviporviridisLitevroomwithrXVector

Readme and manuals

Help Manual

Help pageTopics
HiContacts arithmetics functionalitiesaggregate,HiCExperiment-method arithmetics autocorrelate boost coarsen despeckle detrend divide merge,HiCExperiment,HiCExperiment-method normalize,HiCExperiment-method subsample
cisTransRatiocisTransRatio
ContactsContacts
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 compartmentsgetCompartments
Contact map insulationgetBorders getDiamondInsulation
Finding loops in contact mapgetLoops
HiContacts plotting functionalitiesHiContacts-plots
Matrix palettesafmhotrColors bbrColors bgrColors bwrColors coolerColors palettes rainbowColors
Plotting virtual 4C profilesplot4C
Plotting a contact matrixmontage montage,AggrHiCExperiment-method plotMatrix plotMatrix,AggrHiCExperiment-method plotMatrix,GInteractions-method plotMatrix,HiCExperiment-method plotMatrix,matrix-method
Plotting a P(s) distance lawplotPs plotPsSlope
Plotting saddle plotsplotSaddle
Plotting scalogramsplotScalogram
Compute a scalogram of contactsscalogram
Aligning tracks with HiCExperiment objectscoverage,HiCExperiment-method tracks
Computing virtual 4C profilesvirtual4C