Package: HiCDOC 1.14.0
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:
HiCDOC_1.14.0.tar.gz
HiCDOC_1.14.0.zip(r-4.7)HiCDOC_1.14.0.zip(r-4.6)HiCDOC_1.14.0.zip(r-4.5)
HiCDOC_1.14.0.tgz(r-4.6-x86_64)HiCDOC_1.14.0.tgz(r-4.6-arm64)HiCDOC_1.14.0.tgz(r-4.5-x86_64)HiCDOC_1.14.0.tgz(r-4.5-arm64)
HiCDOC_1.14.0.tar.gz(r-4.7-arm64)HiCDOC_1.14.0.tar.gz(r-4.7-x86_64)HiCDOC_1.14.0.tar.gz(r-4.6-arm64)HiCDOC_1.14.0.tar.gz(r-4.6-x86_64)
HiCDOC_1.14.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HiCDOC/json (API)
NEWS
| # Install 'HiCDOC' in R: |
| install.packages('HiCDOC', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mzytnicki/hicdoc/issues
- exampleHiCDOCDataSet - Example HiCDOCDataSet.
- exampleHiCDOCDataSetProcessed - Example HiCDOCDataSet, filtered, normalized and with compartements detected.
On BioConductor:HiCDOC-1.15.0(bioc 3.24)HiCDOC-1.14.0(bioc 3.23)
hicdna3dstructurenormalizationsequencingsoftwareclusteringzlibcpp
Last updated from:f610dc04c2 (on RELEASE_3_23). Checks:12 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 195 | ||
| linux-devel-arm64 | NOTE | 439 | ||
| linux-devel-x86_64 | NOTE | 487 | ||
| source / vignettes | OK | 362 | ||
| linux-release-arm64 | NOTE | 411 | ||
| linux-release-x86_64 | NOTE | 549 | ||
| macos-release-arm64 | NOTE | 272 | ||
| macos-release-x86_64 | NOTE | 545 | ||
| macos-oldrel-arm64 | NOTE | 385 | ||
| macos-oldrel-x86_64 | NOTE | 714 | ||
| windows-devel | NOTE | 458 | ||
| windows-release | NOTE | 457 | ||
| windows-oldrel | NOTE | 414 | ||
| wasm-release | OK | 163 |
Exports:chromosomescompartmentsconcordancesdefaultHiCDOCParametersdetectCompartmentsdifferencesfilterSmallChromosomesfilterSparseReplicatesfilterWeakPositionsHiCDOCHiCDOCDataSetFromCoolHiCDOCDataSetFromHiCHiCDOCDataSetFromHiCProHiCDOCDataSetFromTabularnormalizeBiologicalBiasesnormalizeDistanceEffectnormalizeTechnicalBiasesparametersparameters<-plotCentroidsplotCompartmentChangesplotCompartmentsplotConcordanceDifferencesplotConcordancesplotDistanceEffectplotInteractionsplotSelfInteractionRatiosreduceHiCDOCDataSetsampleConditionssampleReplicatesshow
Dependencies:abindaggregationaskpassBHBiobaseBiocGenericsbiocmakeBiocParallelcalibrateclicodetoolscowplotcpp11curldata.tableDelayedArraydir.expirydplyredgeRfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablegtoolsHiCcomparehttrInteractionSetIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemultiHiCcomparenlmeopensslpbapplypheatmappillarpkgconfigqqmanR6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| 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 |
