TopDom: An Efficient and Deterministic Method for Identifying Topological Domains in Genomes

The 'TopDom' method identifies topological domains in genomes from Hi-C sequence data (Shin et al., 2016 <doi:10.1093/nar/gkv1505>). The authors published an implementation of their method as an R script (two different versions; also available in this package). This package originates from those original 'TopDom' R scripts and provides help pages adopted from the original 'TopDom' PDF documentation. It also provides a small number of bug fixes to the original code.

Version: 0.10.1
Depends: R (≥ 3.3.0)
Imports: matrixStats, grid, ggplot2, reshape2, tibble
Suggests: diffobj (≥ 0.1.11)
Published: 2021-05-06
Author: Henrik Bengtsson [aut, cre, cph], Hanjun Shin [aut, ctr, cph], Harris Lazaris [ctr, cph] (PhD Student, NYU), Gangqing Hu [ctr, cph] (Staff Scientist, NIH), Xianghong Zhou [ctr]
Maintainer: Henrik Bengtsson <henrikb at braju.com>
BugReports: https://github.com/HenrikBengtsson/TopDom/issues
License: GPL-2 | GPL-3 [expanded from: GPL]
URL: https://github.com/HenrikBengtsson/TopDom
NeedsCompilation: no
Citation: TopDom citation info
Materials: README NEWS
CRAN checks: TopDom results

Documentation:

Reference manual: TopDom.pdf

Downloads:

Package source: TopDom_0.10.1.tar.gz
Windows binaries: r-devel: TopDom_0.10.1.zip, r-release: TopDom_0.10.1.zip, r-oldrel: TopDom_0.10.1.zip
macOS binaries: r-release (arm64): TopDom_0.10.1.tgz, r-release (x86_64): TopDom_0.10.1.tgz, r-oldrel: TopDom_0.10.1.tgz

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