Changes in version 1.5.6: o Relaxed checks in preparePairs(), prepPseudoPairs() when more chromosomes are supplied than needed. o Relaxed checks in connectCounts() when extra chromosomes are in the input ranges. o Fixed an issue with preparePairs() when too many file handles are open. o Fixed clash between BiocGenerics and Matrix which(). o Modified domainDirections() to return a RangedSummarizedExperiment. o Removed defunct DIList class and methods. o Switched from seqlevels() to seqlevelsInUse() for fragment intervals. o Updated user's guide, documentation. Changes in version 1.4.0: o Deprecated DIList objects and methods in favour of InteractionSet objects. o marginCounts() now returns a RangedSummarizedExperiment for all bins. o Added the max.height argument to the rotPlaid() and rotDI() functions. o Added the diClusters() function for post-hoc cluster-level FDR control. o Added the annotatePairs() function for convenient annotation of (clusters of) interactions. o Fixed a bug in plotPlaid() when the interaction space was empty. o Fixed a bug in preparePairs() where unmapped chimeric segments led to the loss of the entire pair. o Updated user's guide, documentation and tests. Changes in version 1.2.0: o Renamed normalize() to normOffsets(). o Added library size specification to DIList methods normOffsets(), asDGEList(). o Fixed bugs under pathological settings in plotPlaid(), plotDI(), rotPlaid(), rotDI(). o Optimized C++ code for connectCounts(), squareCounts(). o Streamlined various R utilities used throughout all functions. o Added iter_map.py to inst/python, for iterative mapping of DNase Hi-C data. o Added the neighborCounts() function, for simultaneous read counting and enrichment calculation. o Added exclude for enrichedPairs(), to provide an exclusion zone in the local neighborhood. o Switched default colour in rotPlaid(), plotPlaid() to black. o Added compartmentalize() function to identify genomic compartments. o Added domainDirections() function to help identify domains. o Modified correctedContact() to allow distance correction and report factorized probabilities directly. o Modified marginCounts() function for proper single-end-like treatment of Hi-C data. o Extended clusterPairs() to merge bin pairs from multiple DILists. o Switched to reporting ranges directly from boxPairs(), added support for minimum bounding box output. o Modified consolidatePairs() to accept index vectors for greater modularity. o Added reference argument for large bin pairs, in filterDirect() and filterTrended(). o Added filterDiag() convenience function for filtering of (near-)diagonal bin pairs. o Slight change to preparePairs() diagnostic reports when dedup=FALSE, and for unpaired reads. o Added option for a distance-based threshold to define invalid chimeras in preparePairs(). o Updated documentation, tests and user's guide. o Added diffHic paper entry to CITATION. Changes in version 1.0.0: o New package diffHic, for detection of differential interactions from Hi-C data.