diffHic: Differential Analyis of Hi-C Data

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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.

Author
Aaron Lun <alun@wehi.edu.au>
Date of publication
None
Maintainer
Aaron Lun <alun@wehi.edu.au>
License
GPL-3
Version
1.6.0

View on Bioconductor

Man pages

annotatePairs
Annotate bin pairs
boxPairs
Put bin pairs into boxes
clusterPairs
Cluster bin pairs
compartmentalize
Identify genomic compartments
connectCounts
Count connecting read pairs
consolidatePairs
Consolidate results for interactions
correctedContact
Iterative correction of Hi-C counts
cutGenome
Cut up the genome
diClusters
Cluster significant bin pairs to DIs
diffHicUsersGuide
View diffHic user's guide
DNaseHiC
Methods for processing DNase Hi-C data
domainDirections
Calculate domain directionality
enrichedPairs
Compute local enrichment for bin pairs
filterDiag
Filtering of diagonal bin pairs
filterPeaks
Filter bin pairs for likely peaks
filters
Filtering strategies for bin pairs
getArea
Get interaction area
getPairData
Get read pair data
loadData
Load data from an index file
marginCounts
Collect marginal counts for each bin
mergePairs
Merge read pairs
neighborCounts
Load Hi-C interaction counts
normalizeCNV
Normalize CNV biases
pairParam
pairParam class and methods
plotDI
Construct a plaid plot of differential interactions
plotPlaid
Construct a plaid plot of interactions
preparePairs
Prepare Hi-C pairs
prunePairs
Prune read pairs
savePairs
Save Hi-C interactions
squareCounts
Load Hi-C interaction counts
totalCounts
Get the total counts

Files in this package

diffHic/DESCRIPTION
diffHic/NAMESPACE
diffHic/R
diffHic/R/annotatePairs.R
diffHic/R/boxPairs.R
diffHic/R/clusterPairs.R
diffHic/R/compartmentalize.R
diffHic/R/connectCounts.R
diffHic/R/consolidatePairs.R
diffHic/R/correctedContact.R
diffHic/R/cutGenome.R
diffHic/R/diClusters.R
diffHic/R/diffHicUsersGuide.R
diffHic/R/domainDirections.R
diffHic/R/filterPeaks.R
diffHic/R/filters.R
diffHic/R/getArea.R
diffHic/R/getPairData.R
diffHic/R/h5utils.R
diffHic/R/marginCounts.R
diffHic/R/mergePairs.R
diffHic/R/neighborCounts.R
diffHic/R/normalizeCNV.R
diffHic/R/pairParam.R
diffHic/R/plotPlaid.R
diffHic/R/prepPseudoPairs.R
diffHic/R/preparePairs.R
diffHic/R/prunePairs.R
diffHic/R/rotPlaid.R
diffHic/R/savePairs.R
diffHic/R/squareCounts.R
diffHic/R/totalCounts.R
diffHic/build
diffHic/build/vignette.rds
diffHic/inst
diffHic/inst/CITATION
diffHic/inst/NEWS.Rd
diffHic/inst/doc
diffHic/inst/doc/bam2hdf.R
diffHic/inst/doc/diffHic.Rnw
diffHic/inst/doc/diffHic.pdf
diffHic/inst/doc/diffHicUsersGuide.pdf
diffHic/inst/doc/sra2bam.sh
diffHic/inst/exdata
diffHic/inst/exdata/cuts.rds
diffHic/inst/exdata/generator.R
diffHic/inst/exdata/hic_sort.bam
diffHic/inst/python
diffHic/inst/python/iter_map.py
diffHic/inst/python/presplit_map.py
diffHic/inst/tests
diffHic/inst/tests/run_all_tests.sh
diffHic/inst/tests/simcounts.R
diffHic/inst/tests/simsam.R
diffHic/inst/tests/test-anno.R
diffHic/inst/tests/test-anno.Rout.save
diffHic/inst/tests/test-box.R
diffHic/inst/tests/test-box.Rout.save
diffHic/inst/tests/test-cluster.R
diffHic/inst/tests/test-cluster.Rout.save
diffHic/inst/tests/test-connect.R
diffHic/inst/tests/test-connect.Rout.save
diffHic/inst/tests/test-cut.R
diffHic/inst/tests/test-cut.Rout.save
diffHic/inst/tests/test-diclust.R
diffHic/inst/tests/test-diclust.Rout.save
diffHic/inst/tests/test-domains.R
diffHic/inst/tests/test-domains.Rout.save
diffHic/inst/tests/test-empty.R
diffHic/inst/tests/test-empty.Rout.save
diffHic/inst/tests/test-filter.R
diffHic/inst/tests/test-filter.Rout.save
diffHic/inst/tests/test-hic-pair.R
diffHic/inst/tests/test-hic-pair.Rout.save
diffHic/inst/tests/test-interactions.R
diffHic/inst/tests/test-interactions.Rout.save
diffHic/inst/tests/test-itercor.R
diffHic/inst/tests/test-itercor.Rout.save
diffHic/inst/tests/test-margin.R
diffHic/inst/tests/test-margin.Rout.save
diffHic/inst/tests/test-neighbor.R
diffHic/inst/tests/test-neighbor.Rout.save
diffHic/inst/tests/test-pair-manip.R
diffHic/inst/tests/test-pair-manip.Rout.save
diffHic/man
diffHic/man/DNaseHiC.Rd
diffHic/man/annotatePairs.Rd
diffHic/man/boxPairs.Rd
diffHic/man/clusterPairs.Rd
diffHic/man/compartmentalize.Rd
diffHic/man/connectCounts.Rd
diffHic/man/consolidatePairs.Rd
diffHic/man/correctedContact.Rd
diffHic/man/cutGenome.Rd
diffHic/man/diClusters.Rd
diffHic/man/diffHicUsersGuide.Rd
diffHic/man/domainDirections.Rd
diffHic/man/enrichedPairs.Rd
diffHic/man/filterDiag.Rd
diffHic/man/filterPeaks.Rd
diffHic/man/filters.Rd
diffHic/man/getArea.Rd
diffHic/man/getPairData.Rd
diffHic/man/loadData.Rd
diffHic/man/marginCounts.Rd
diffHic/man/mergePairs.Rd
diffHic/man/neighborCounts.Rd
diffHic/man/normalizeCNV.Rd
diffHic/man/pairParam.Rd
diffHic/man/plotDI.Rd
diffHic/man/plotPlaid.Rd
diffHic/man/preparePairs.Rd
diffHic/man/prunePairs.Rd
diffHic/man/savePairs.Rd
diffHic/man/squareCounts.Rd
diffHic/man/totalCounts.Rd
diffHic/src
diffHic/src/Makevars
diffHic/src/Makevars.win
diffHic/src/binner.cpp
diffHic/src/check_input.cpp
diffHic/src/cluster_2d.cpp
diffHic/src/count_background.cpp
diffHic/src/count_connect.cpp
diffHic/src/count_patch.cpp
diffHic/src/diffhic.h
diffHic/src/directionality.cpp
diffHic/src/init.cpp
diffHic/src/iterative_correction.cpp
diffHic/src/nb_average.cpp
diffHic/src/neighbors.cpp
diffHic/src/neighbors.h
diffHic/src/pair_stats.cpp
diffHic/src/quadrant_bg.cpp
diffHic/src/read_count.h
diffHic/src/report_hic_pairs.cpp
diffHic/src/trended_filter.cpp
diffHic/tests
diffHic/tests/test-basic.R
diffHic/tests/test-basic.Rout.save
diffHic/vignettes
diffHic/vignettes/diffHic.Rnw