diffHic: Differential Analyis 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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("diffHic")
AuthorAaron Lun <alun@wehi.edu.au>
Bioconductor views Alignment Clustering Coverage HiC MultipleComparison Normalization Preprocessing Sequencing
Date of publicationNone
MaintainerAaron Lun <alun@wehi.edu.au>
LicenseGPL-3
Version1.6.0

View on Bioconductor

Functions

annotatePairs Man page
boxPairs Man page
clusterPairs Man page
compartmentalize Man page
connectCounts Man page
consolidatePairs Man page
correctedContact Man page
cutGenome Man page
diClusters Man page
diffHic Man page
diffHicUsersGuide Man page
domainDirections Man page
enrichedPairs Man page
filterDiag Man page
filterDirect Man page
filterPeaks Man page
filterTrended Man page
getArea Man page
getPairData Man page
loadChromos Man page
loadData Man page
marginCounts Man page
matchMargins Man page
mergePairs Man page
neighborCounts Man page
normalizeCNV Man page
pairParam Man page
pairParam-class Man page
$,pairParam-method Man page
plotDI Man page
plotPlaid Man page
preparePairs Man page
prepPseudoPairs Man page
prunePairs Man page
reform Man page
reform,pairParam-method Man page
rotDI Man page
rotPlaid Man page
savePairs Man page
segmentGenome Man page
show,pairParam-method Man page
squareCounts Man page
totalCounts Man page

Files

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

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