hbm: Hierarchical Block Matrix Analysis

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A package for building hierarchical block matrices from association matrices and for performing multi-scale analysis. It specifically targets chromatin contact maps, generated from high-throughput chromosome conformation capture data, such as 5C and Hi-C, and provides methods for detecting movements and for computing chain hierarchy and region communicability across scales.

Author
Yoli Shavit
Date of publication
2015-02-01 19:50:29
Maintainer
Yoli Shavit <ys388@cam.ac.uk>
License
GPL (>= 2)
Version
1.0

View on CRAN

Man pages

add.noise
Add Noise to a Symmetric Association Matrix
communicability
Compute Communicability between Nodes in an HBM
detect.movement
Detect Movements Between Association Matrices using their...
generate.random.conf
Generate a Random Chain Configuration
get.movements
Summarize Detected Movements
hbm
Build a Hierarchical Block Matrix (HBM)
hbm.features
Compute Robust Features in an HBM
hbm-package
Hierarchical Block Matrix Analysis
hierarchy
Compute Hierarchy of an HBM
mcl
Markov Clustering

Files in this package

hbm
hbm/NAMESPACE
hbm/R
hbm/R/hbm.R
hbm/MD5
hbm/DESCRIPTION
hbm/man
hbm/man/add.noise.Rd
hbm/man/hbm.Rd
hbm/man/communicability.Rd
hbm/man/hierarchy.Rd
hbm/man/hbm.features.Rd
hbm/man/generate.random.conf.Rd
hbm/man/mcl.Rd
hbm/man/hbm-package.Rd
hbm/man/get.movements.Rd
hbm/man/detect.movement.Rd