HiCblock

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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Description file content

Package
HiCblock
Type
Package
Title
Systematic Analysis of Architectural Proteins and Functional Elements in Blocking Long-Range Contacts Between Loci
Version
1.4
Depends
R (>= 3.4.0)
Imports
IRanges, GenomeInfoDb, methods, GenomicRanges, Matrix, glmnet, rtracklayer, HiTC, MASS, S4Vectors
Date
2018-04-18
Author
Raphael Mourad
Maintainer
Raphael Mourad
Description
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.
License
GPL-2
NeedsCompilation
no
Packaged
2018-04-18 18:29:41 UTC; mourad
Repository
CRAN
Date/Publication
2018-04-18 22:46:01 UTC

install.packages('HiCblock')

1.4

3 months ago

Raphael Mourad

GPL-2

Depends on

R (>= 3.4.0)

Imports

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

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