SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.
|Author||Kellen Cresswell <[email protected]>, John Stansfield <[email protected]>, Mikhail Dozmorov <[email protected]>|
|Bioconductor views||Clustering FeatureExtraction HiC Sequencing Software|
|Maintainer||Kellen Cresswell <[email protected]>|
|License||MIT + file LICENSE|
|Package repository||View on GitHub|
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