Package: diffHic 1.41.0

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

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diffHic.pdf |diffHic.html✨
diffHic/json (API)
NEWS

# Install 'diffHic' in R:

install.packages('diffHic', repos = c('https://bioc.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-1.43.0(bioc 3.23)diffHic-1.42.0(bioc 3.22)

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

multiplecomparison preprocessing sequencing coverage alignment normalization clustering hic curl bzip2 xz-utils zlib cpp

6.13 score 1 packages 45 scripts 464 downloads 12 mentions 43 exports 62 dependencies

Last updated from:45164073de. Checks:1 ERROR, 11 NOTE, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Total time
bioc-checks	ERROR	238
linux-devel-arm64	NOTE	403
linux-devel-x86_64	NOTE	406
source / vignettes	OK	377
linux-release-arm64	NOTE	390
linux-release-x86_64	NOTE	444
macos-release-arm64	NOTE	258
macos-release-x86_64	NOTE	774
macos-oldrel-arm64	NOTE	498
macos-oldrel-x86_64	NOTE	751
windows-devel	NOTE	587
windows-release	NOTE	480
windows-oldrel	NOTE	510
wasm-release	FAIL	239

Exports:annotatePairs asDGEList boxPairs clusterPairs compartmentalize connectCounts consolidatePairs correctedContact cutGenome diClusters diffHicUsersGuide domainDirections emptyGenome enrichedPairs extractPatch filterDiag filterDirect filterPeaks filterTrended getArea getPairData loadChromos loadData marginCounts matchMargins mergeCMs mergePairs neighborCounts normalizeCNV pairParam plotDI plotPlaid preparePairs prepPseudoPairs prunePairs readMTX2IntSet reform rotDI rotPlaid savePairs segmentGenome squareCounts totalCounts

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cigarillo codetools cpp11 crayon csaw curl DelayedArray edgeR formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges httr InteractionSet IRanges jsonlite lambda.r lattice limma locfit Matrix MatrixGenerics matrixStats metapod mime openssl R6 Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray statmod SummarizedExperiment sys UCSC.utils XML XVector yaml

diffHic Vignette

Rendered fromdiffHic.Rnwusingutils::Sweaveon Nov 23 2025.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate bin pairs	annotatePairs
Put bin pairs into boxes	boxPairs
Cluster bin pairs	clusterPairs
Identify genomic compartments	compartmentalize
Count connecting read pairs	connectCounts
Consolidate results for interactions	consolidatePairs
Iterative correction of Hi-C counts	correctedContact
Cut up the genome	cutGenome
Cluster significant bin pairs to DIs	diClusters
View diffHic user's guide	diffHic diffHicUsersGuide
Methods for processing DNase Hi-C data	emptyGenome prepPseudoPairs segmentGenome
Calculate domain directionality	domainDirections
Collect local enrichment statistics for bin pairs	enrichedPairs
Extract a patch of the interaction space	extractPatch
Filtering of diagonal bin pairs	filterDiag
Filtering strategies for bin pairs	filterDirect filterTrended
Filter bin pairs for likely peaks	filterPeaks
Get interaction area	getArea
Get read pair data	getPairData
Load data from an index file	loadChromos loadData
Collect marginal counts for each bin	marginCounts
Merge ContactMatrix objects	mergeCMs
Merge read pairs	mergePairs
Load Hi-C interaction counts	neighborCounts
Normalize CNV biases	matchMargins normalizeCNV
pairParam class and methods	$,pairParam-method pairParam pairParam-class reform reform,pairParam-method show,pairParam-method
Construct a plaid plot of differential interactions	plotDI rotDI
Construct a plaid plot of interactions	plotPlaid rotPlaid
Prepare Hi-C pairs	preparePairs
Prune read pairs	prunePairs
Create an InteractionSet from a BED file and Matrix Market files	readMTX2IntSet
Save Hi-C read pairs	savePairs
Load Hi-C interaction counts	squareCounts
Get the total counts	totalCounts