Systematic Analysis of Architectural Proteins and Functional Elements in Blocking Long-Range Contacts Between Loci

Here we propose a model to systematically analyze the roles of architectural proteins and functional elements in blocking long-range contacts between loci. The proposed model does not rely on topologically associating domain (TAD) mapping from Hi-C data. Instead of testing the enrichment or influence of protein binding at TAD borders, the model directly estimates the blocking effect of proteins on long-range contacts between flanking loci, making the model intuitive and biologically meaningful.


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1.4 by Raphael Mourad, a year ago

Browse source code at

Authors: Raphael Mourad

Documentation:   PDF Manual  

GPL-2 license

Imports IRanges, GenomeInfoDb, methods, GenomicRanges, Matrix, glmnet, rtracklayer, HiTC, MASS, S4Vectors

See at CRAN