diffHic: Differential Analyis of Hi-C Data
Version 1.8.1

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.

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
Version1.8.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("diffHic")

Popular man pages

consolidatePairs: Consolidate results for interactions
correctedContact: Iterative correction of Hi-C counts
diClusters: Cluster significant bin pairs to DIs
diffHicUsersGuide: View diffHic user's guide
mergePairs: Merge read pairs
pairParam: pairParam class and methods
squareCounts: Load Hi-C interaction counts
See all...

All man pages Function index File listing

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

Functions

Files

DESCRIPTION
NAMESPACE
R
R/annotatePairs.R
R/basefun.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/enrichedPairs.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-dnase.R
inst/tests/test-dnase.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
inst/tests/test-prune.R
inst/tests/test-prune.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/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
diffHic documentation built on May 20, 2017, 10:52 p.m.

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