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.
| Version: | 1.4 |
| Depends: | R (≥ 3.4.0) |
| Imports: | IRanges, GenomeInfoDb, methods, GenomicRanges, Matrix, glmnet, rtracklayer, HiTC, MASS, S4Vectors |
| Published: | 2018-04-18 |
| Author: | Raphael Mourad |
| Maintainer: | Raphael Mourad <raphael.mourad at ibcg.biotoul.fr> |
| License: | GPL-2 |
| NeedsCompilation: | no |
| CRAN checks: | HiCblock results |
| Reference manual: | HiCblock.pdf |
| Package source: | HiCblock_1.4.tar.gz |
| Windows binaries: | r-devel: HiCblock_1.4.zip, r-release: HiCblock_1.4.zip, r-oldrel: HiCblock_1.4.zip |
| OS X binaries: | r-release: not available, r-oldrel: HiCblock_1.4.tgz |
| Old sources: | HiCblock archive |
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