DIList-class            DIList class and methods
boxPairs                Put bin pairs into boxes
clusterPairs            Cluster bin pairs
connectCounts           Count connecting read pairs
consolidatePairs        Consolidate results for bin pairs
correctedContact        Iterative correction of Hi-C counts
cutGenome               Cut up the genome
diffHicUsersGuide       View diffHic user's guide
enrichedPairs           Compute local enrichment for bin pairs
filterDirect            Filtering strategies for bin pairs
filterPeaks             Filter bin pairs for likely peaks
getArea                 Get interaction area
getDistance             Get the linear distance for each interaction
getPairData             Get read pair data
loadData                Load data from an index file
marginCounts            Collect marginal counts for each bin
mergePairs              Merge read pairs
normalizeCNV            Normalize CNV biases
pairParam               pairParam class and methods
plotDI                  Construct a plaid plot of differential
                        interactions
plotPlaid               Construct a plaid plot of interactions
prepPseudoPairs         Methods for processing DNase Hi-C data
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
