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chevron_left Differential genomic interaction detection Normalization Bioinformatics workflows Heatmap generation Read alignment chevron_right

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diffHic specifications


Unique identifier OMICS_09658
Name diffHic
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data HDF5 files
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.12.1
Stability Stable
limma, methods, stats, graphics, BiocGenerics, IRanges, GenomicRanges, Rsamtools, Matrix, utils, S4Vectors, GenomeInfoDb, Biostrings, grDevices, R(>=3.5), SummarizedExperiment, edgeR, locfit, Rcpp, BSgenome, BSgenome.Ecoli.NCBI.20080805, Rhtslib, rhdf5, InteractionSet, csaw
Maintained Yes


No version available



  • person_outline Aaron Lun <>

Publication for diffHic

diffHic citations


Software tools for visualizing Hi C data

PMCID: 5290626
PMID: 28159004
DOI: 10.1186/s13059-017-1161-y

[…] data, but other transformations of the data can be visualized using the same set of tools. for example, statistical confidence measures, such as p-values produced by methods such as fit-hi-c [] or diffhic [], can be converted to a contact matrix format and then visualized using the tools reviewed here. hi-c data also can be used to infer the 3d structure of the chromatin (methods reviewed […]


Capturing genomic relationships that matter

PMCID: 5346121
PMID: 28078515
DOI: 10.1007/s10577-016-9546-4

[…] provide context of interactions., an alternative analysis aims to identify functional interactions by characterising differential contacts between two cell types or conditions. homer, hibrowse and diffhic were developed for detecting differential interactions in hic data, built upon previous methods that were originally applied to identify differentially expressed genes in rna-seq data (e.g. […]

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diffHic institution(s)
The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Melbourne, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Melbourne, Australia; Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Melbourne, Australia

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