DIList-class
(Package: diffHic) :
DIList class and methods
Using the DIList class to store pairwise genomic interactions.
● Data Source:
BioConductor
● Keywords: counting
● Alias: DIList, DIList-class
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DNaseHiC
(Package: diffHic) :
Methods for processing DNase Hi-C data
Processing of BAM files for DNase Hi-C into index files
● Data Source:
BioConductor
● Keywords: preprocessing
● Alias: prepPseudoPairs, segmentGenome
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0 images
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Annotate bin pairs based on features overlapping the anchor regions.
● Data Source:
BioConductor
● Keywords: annotation
● Alias: annotatePairs
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0 images
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boxPairs
(Package: diffHic) :
Put bin pairs into boxes
Match smaller bin pairs to the larger bin pairs in which they are nested.
● Data Source:
BioConductor
● Keywords: clustering
● Alias: boxPairs
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Aggregate bin pairs into local clusters for summarization.
● Data Source:
BioConductor
● Keywords: clustering
● Alias: clusterPairs
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Use contact matrices to identify self-interacting genomic compartments
● Data Source:
BioConductor
● Keywords: clustering
● Alias: compartmentalize
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connectCounts
(Package: diffHic) :
Count connecting read pairs
Count the number of read pairs connecting pairs of user-specified regions
● Data Source:
BioConductor
● Keywords: counting
● Alias: connectCounts
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0 images
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consolidatePairs
(Package: diffHic) :
Consolidate results for interactions
Consolidate differential testing results for interactions from separate analyses.
● Data Source:
BioConductor
● Keywords: testing
● Alias: consolidatePairs
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0 images
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correctedContact
(Package: diffHic) :
Iterative correction of Hi-C counts
Perform iterative correction on counts for Hi-C interactions to correct for biases between fragments.
● Data Source:
BioConductor
● Keywords: normalization
● Alias: correctedContact
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1 images
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Perform an in silico restriction digest of a target genome.
● Data Source:
BioConductor
● Keywords: preprocessing
● Alias: cutGenome
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providing 
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