Chicdiff: Differential analysis of Capture Hi-C data

Chicdiff is a statistical pipeline for calling differential chromosomal interactions in Capture Hi-C data. It is intended to be used in conjunction with CHiCAGO – our tool for calling significant interactions in Capture Hi-C data from a single condition.

The Chicdiff methodology

Chicdiff combines moderated differential testing for count data implemented in DESeq2 with CHi-C-specific procedures for signal normalisation and p-value weighting. To increase power, Chicdiff also combines reads across several fragments surrounding each significantly interacting region for each bait. Chicdiff takes as input CHiCAGO-processed data for each replicate and condition and uses the parameters learned by CHiCAGO in data normalisation. Please refer to the package vignette and paper for more details.

The software

Chicdiff is implemented in the form of an open-source R package of the same name. In addition, we provide a data package (ChicdiffData) with subsets of published Promoter Capture HiC datasets for training purposes. Both packages, along with detailed documentation, are available from the following github repository:


The Chicdiff package vignette in HTML format can also be viewed here (opens in a new window).

The paper

The paper presenting Chicdiff is currently available as a preprint:

Cairns J* / Orchard WR* / Malysheva V* and Spivakov M. Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data. bioRxiv 2019 https://doi.org/10.1101/526269.


CHiCAGO has been co-developed by Jonathan Cairns, William Orchard, Valeriya Malysheva (joint lead authors) and Mikhail Spivakov in the Regulatory Genomics group at Babraham Institute and Functional Gene Control group at MRC LMS / Imperial College following our move to London.


For specific issues, please submit a report on Github:


If you have any general feedback on Chicdiff or would like to collaborate, please don’t hesitate to contact to Mikhail (mikhail.spivakov/lms.mrc.ac.uk).

Chicdiff example