Package: HiCDOC 1.15.2

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_1.15.2.tar.gz
HiCDOC_1.15.2.zip(r-4.7)HiCDOC_1.15.2.zip(r-4.6)HiCDOC_1.15.2.zip(r-4.5)
HiCDOC_1.15.2.tgz(r-4.6-x86_64)HiCDOC_1.15.2.tgz(r-4.6-arm64)HiCDOC_1.15.2.tgz(r-4.5-x86_64)HiCDOC_1.15.2.tgz(r-4.5-arm64)
HiCDOC_1.15.2.tar.gz(r-4.7-arm64)HiCDOC_1.15.2.tar.gz(r-4.7-x86_64)HiCDOC_1.15.2.tar.gz(r-4.6-arm64)HiCDOC_1.15.2.tar.gz(r-4.6-x86_64)
HiCDOC_1.15.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HiCDOC/json (API)

# Install 'HiCDOC' in R:

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

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

exampleHiCDOCDataSet - Example HiCDOCDataSet.
exampleHiCDOCDataSetProcessed - Example HiCDOCDataSet, filtered, normalized and with compartements detected.

On BioConductor:HiCDOC-1.15.1(bioc 3.24)HiCDOC-1.14.0(bioc 3.23)

hic dna3dstructure normalization sequencing software clustering cpp

5.78 score 5 stars 6 scripts 346 downloads 31 exports 87 dependencies

Last updated from:2c0c315182. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	230
linux-devel-arm64	NOTE	406
linux-devel-x86_64	NOTE	499
source / vignettes	OK	332
linux-release-arm64	NOTE	382
linux-release-x86_64	NOTE	477
macos-release-arm64	NOTE	382
macos-release-x86_64	NOTE	488
macos-oldrel-arm64	NOTE	334
macos-oldrel-x86_64	NOTE	583
windows-devel	NOTE	341
windows-release	NOTE	437
windows-oldrel	NOTE	418
wasm-release	OK	160

Exports:chromosomes compartments concordances defaultHiCDOCParameters detectCompartments differences filterSmallChromosomes filterSparseReplicates filterWeakPositions HiCDOC HiCDOCDataSetFromCool HiCDOCDataSetFromHiC HiCDOCDataSetFromHiCPro HiCDOCDataSetFromTabular normalizeBiologicalBiases normalizeDistanceEffect normalizeTechnicalBiases parameters parameters<-plotCentroids plotCompartmentChanges plotCompartments plotConcordanceDifferences plotConcordances plotDistanceEffect plotInteractions plotSelfInteractionRatios reduceHiCDOCDataSet sampleConditions sampleReplicates show

Dependencies:abind aggregation askpass BH Biobase BiocGenerics biocmake BiocParallel calibrate cli codetools cowplot cpp11 curl data.table DelayedArray dir.expiry dplyr edgeR farver filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable gtools HiCcompare HiCParser httr InteractionSet IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime multiHiCcompare nlme openssl pbapply pheatmap pillar pkgconfig qqman R6 RColorBrewer Rcpp rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector

HiCDOC

Rendered fromHiCDOC.Rmdusingknitr::rmarkdown

Last update: 2026-05-26
Started: 2020-10-08

Help page	Topics
A/B compartment detection and differential analysis	HiCDOC-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

Package: HiCDOC 1.15.2

HiCDOC: A/B compartment detection and differential analysis

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