Package: HiCDOC 1.7.0

Maigné Élise

HiCDOC: A/B compartment detection and differential analysis

HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.

Authors:Kurylo Cyril [aut], Zytnicki Matthias [aut], Foissac Sylvain [aut], Maigné Élise [aut, cre]

HiCDOC_1.7.0.tar.gz
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HiCDOC.pdf |HiCDOC.html✨
HiCDOC/json (API)
NEWS

# Install 'HiCDOC' in R:
install.packages('HiCDOC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mzytnicki/hicdoc/issues

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:HiCDOC-1.7.0(bioc 3.20)HiCDOC-1.6.0(bioc 3.19)

bioconductor-package

31 exports 1.24 score 86 dependencies 1 dependents

Last updated 2 months agofrom:7216e6511b

Exports:chromosomescompartmentsconcordancesdefaultHiCDOCParametersdetectCompartmentsdifferencesfilterSmallChromosomesfilterSparseReplicatesfilterWeakPositionsHiCDOCHiCDOCDataSetFromCoolHiCDOCDataSetFromHiCHiCDOCDataSetFromHiCProHiCDOCDataSetFromTabularnormalizeBiologicalBiasesnormalizeDistanceEffectnormalizeTechnicalBiasesparametersparameters<-plotCentroidsplotCompartmentChangesplotCompartmentsplotConcordanceDifferencesplotConcordancesplotDistanceEffectplotInteractionsplotSelfInteractionRatiosreduceHiCDOCDataSetsampleConditionssampleReplicatesshow

Dependencies:abindaggregationaskpassBHBiobaseBiocGenericsBiocParallelcalibrateclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDelayedArraydplyredgeRfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablegtoolsHiCcomparehttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemultiHiCcomparemunsellnlmeopensslpbapplypheatmappillarpkgconfigqqmanR6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsscalessnowSparseArraystatmodSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

HiCDOC

Cyril Kurylo & Matthias Zytnicki & Sylvain Foissac & Elise Maigné

Rendered fromHiCDOC.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-09-06
Started: 2020-10-08

Readme and manuals

Help Manual

Help pageTopics
A/B compartment detection and differential analysisHiCDOC-package _PACKAGE
A and B compartments detection and differences across conditions.detectCompartments
Example HiCDOCDataSet.exampleHiCDOCDataSet
Example HiCDOCDataSet, filtered, normalized and with compartements detected.exampleHiCDOCDataSetProcessed
Filter small chromosomes.filterSmallChromosomes
Filter sparse replicates.filterSparseReplicates
Filter weak positions.filterWeakPositions
Default pipeline to run on the HiCDOC analysis.HiCDOC
'HiCDOCDataSet' S4 class.HiCDOCDataSet HiCDOCDataSet-class
Methods to access a 'HiCDOCDataSet' components.chromosomes chromosomes,HiCDOCDataSet-method compartments compartments,HiCDOCDataSet-method concordances concordances,HiCDOCDataSet-method differences differences,HiCDOCDataSet-method HiCDOCDataSet-methods sampleConditions sampleConditions,HiCDOCDataSet-method sampleReplicates sampleReplicates,HiCDOCDataSet-method show,HiCDOCDataSet-method
Access the parameters of a 'HiCDOCDataSet'.defaultHiCDOCParameters HiCDOCDataSet-parameters parameters parameters,HiCDOCDataSet-method parameters<- parameters<-,HiCDOCDataSet-method
'HiCDOCDataSet' constructor from Cool files.HiCDOCDataSetFromCool
'HiCDOCDataSet' constructor from HiC files.HiCDOCDataSetFromHiC
'HiCDOCDataSet' constructor from HiC-Pro files.HiCDOCDataSetFromHiCPro
'HiCDOCDataSet' constructor from a tabular file.HiCDOCDataSetFromTabular
Normalize biological biases.normalizeBiologicalBiases
Normalize distance effect.normalizeDistanceEffect
Normalize technical biases.normalizeTechnicalBiases
Plot centroids.plotCentroids
Plot compartment changes.plotCompartmentChanges
Plot A/B compartments.plotCompartments
Plot the distribution of concordance differences.plotConcordanceDifferences
Plot concordances.plotConcordances
Plot the distance effect.plotDistanceEffect
Plot interaction matrices.plotInteractions
Plot boxplots of self interaction ratios.plotSelfInteractionRatios
Reduce a 'HiCDOCDataSet'.reduceHiCDOCDataSet