Package: diffHic 1.44.0

Aaron Lun

diffHic: Differential Analysis of Hi-C Data

Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.

Authors:Aaron Lun, Gordon Smyth

diffHic_1.44.0.tar.gz
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diffHic_1.44.0.tgz(r-4.6-x86_64)diffHic_1.44.0.tgz(r-4.6-arm64)diffHic_1.44.0.tgz(r-4.5-x86_64)diffHic_1.44.0.tgz(r-4.5-arm64)
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manual.pdf |manual.html✨
card.svg |card.png
diffHic/json (API)
NEWS

# Install 'diffHic' in R:
install.packages('diffHic', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:diffHic-1.45.0(bioc 3.24)diffHic-1.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

multiplecomparisonpreprocessingsequencingcoveragealignmentnormalizationclusteringhiccurlbzip2xz-utilszlibcpp

6.16 score 1 packages 48 scripts 539 downloads 12 mentions 43 exports 65 dependencies

Last updated from:b22054b515 (on RELEASE_3_23). Checks:1 ERROR, 11 WARNING, 1 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
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linux-devel-x86_64WARNING481
source / vignettesOK425
linux-release-arm64WARNING398
linux-release-x86_64WARNING509
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wasm-releaseFAIL228

Exports:annotatePairsasDGEListboxPairsclusterPairscompartmentalizeconnectCountsconsolidatePairscorrectedContactcutGenomediClustersdiffHicUsersGuidedomainDirectionsemptyGenomeenrichedPairsextractPatchfilterDiagfilterDirectfilterPeaksfilterTrendedgetAreagetPairDataloadChromosloadDatamarginCountsmatchMarginsmergeCMsmergePairsneighborCountsnormalizeCNVpairParamplotDIplotPlaidpreparePairsprepPseudoPairsprunePairsreadMTX2IntSetreformrotDIrotPlaidsavePairssegmentGenomesquareCountstotalCounts

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomecigarillocodetoolscpp11crayoncsawcurlDelayedArraydir.expiryedgeRfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangeshttrInteractionSetIRangesjsonlitelambda.rlatticelimmalocfitMatrixMatrixGenericsmatrixStatsmetapodmimeopensslR6RcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystatmodSummarizedExperimentsysUCSC.utilsXMLXVectoryaml

diffHic Vignette

Rendered fromdiffHic.Rnwusingutils::Sweaveon May 29 2026.

Last update: 2015-07-19
Started: 2015-04-06

Readme and manuals

Help Manual

Help pageTopics
Annotate bin pairsannotatePairs
Put bin pairs into boxesboxPairs
Cluster bin pairsclusterPairs
Identify genomic compartmentscompartmentalize
Count connecting read pairsconnectCounts
Consolidate results for interactionsconsolidatePairs
Iterative correction of Hi-C countscorrectedContact
Cut up the genomecutGenome
Cluster significant bin pairs to DIsdiClusters
View diffHic user's guidediffHic diffHicUsersGuide
Methods for processing DNase Hi-C dataemptyGenome prepPseudoPairs segmentGenome
Calculate domain directionalitydomainDirections
Collect local enrichment statistics for bin pairsenrichedPairs
Extract a patch of the interaction spaceextractPatch
Filtering of diagonal bin pairsfilterDiag
Filtering strategies for bin pairsfilterDirect filterTrended
Filter bin pairs for likely peaksfilterPeaks
Get interaction areagetArea
Get read pair datagetPairData
Load data from an index fileloadChromos loadData
Collect marginal counts for each binmarginCounts
Merge ContactMatrix objectsmergeCMs
Merge read pairsmergePairs
Load Hi-C interaction countsneighborCounts
Normalize CNV biasesmatchMargins normalizeCNV
pairParam class and methods$,pairParam-method pairParam pairParam-class reform reform,pairParam-method show,pairParam-method
Construct a plaid plot of differential interactionsplotDI rotDI
Construct a plaid plot of interactionsplotPlaid rotPlaid
Prepare Hi-C pairspreparePairs
Prune read pairsprunePairs
Create an InteractionSet from a BED file and Matrix Market filesreadMTX2IntSet
Save Hi-C read pairssavePairs
Load Hi-C interaction countssquareCounts
Get the total countstotalCounts