CHiCAGO
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Application data |
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| Created by | Jonathan Cairns, Paula Freire Pritchett, Mikhail Spivakov |
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| Biological application domain(s) | Epigenomics |
| Principal bioinformatics method(s) | Peak calling |
| Technology | Any |
| Created at | Babraham Institute, Cambridge |
| Maintained? | Yes |
| Input format(s) | BAM |
| Output format(s) | iBed, SeqMonk, washU |
| Programming language(s) | R, Python |
| Interface type(s) | Command line |
| Resource type(s) | Command-line tool |
| Licence | Artistic-2.0 |
| Operating system(s) | Linux, OSX |
Summary: CHiCAGO (Capture HiC Analysis of Genomic Organization) is a set of tools for calling significant interactions in Capture HiC data, such as Promoter Capture HiC.
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Description
CHiCAGO uses a convolution noise model accounting for both ‘Brownian’ (distance-dependent) and ‘technical’ noise. It borrows information across interactions (with appropriate normalisation) to estimate these noise components separately on different subsets of data.
CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges (estimated from data), with scores representing soft-thresholded -log weighted p-values.
CHiCAGO consists of an open-source R package (Chicago), a data package with subsets of published Promoter Capture HiC datasets for training purposes (PCHiCdata) and a set of command line tools for pre-processing and post-processing (chicagoTools). All of these, along with detailed documentation, are available from this bitbucket repository:
https://bitbucket.org/chicagoTeam/chicago
Links
References
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