TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes

This is an R package that originates from the original TopDom R script by Shin et al. (2016). This package was put together by Henrik Bengtsson independently of the TopDom authors based on that original TopDom R script and the original TopDom PDF documentation.

The original R script (versions 0.0.1 and 0.0.2) and the TopDom documentation were made available on a website of the TopDom author (http://zhoulab.usc.edu/TopDom/). As of 2019, that website is no longer available. This Git repository holds verbatim copies of the two iterations of the original TopDom R script: TopDom_v0.0.1.R and TopDom_v0.0.2.R, as well as the original TopDom documentation TopDom Manual_v0.0.2.pdf.

The TopDom package is licensed under the GNU Public License (GPL) (per email from XJ Zhou on 2018-11-12).

Installation

This package is only available from GitHub - it is neither on CRAN nor on Bioconductor. To install this package, use:

remotes::install_github("HenrikBengtsson/TopDom")

To get the example data, install the TopDomData package.

Citing TopDom - the method and the package

Whenever using the TopDom method, please cite:

• Hanjun Shin, Yi Shi, Chao Dai, Harianto Tjong, Ke Gong, Frank Alber, Xianghong Jasmine Zhou; TopDom: an efficient and deterministic method for identifying topological domains in genomes, Nucleic Acids Research, Volume 44, Issue 7, 20 April 2016, Pages e70, 10.1093/nar/gkv1505. PMCID: PMC4838359, PMID: 26704975.

Whenever using the TopDom package, please cite:

• Henrik Bengtsson and Hanjun Shin (2018). R Package TopDom: An Efficient and Deterministic Method for Identifying Topological Domains in Genomes. R package version 0.8.1. https://github.com/HenrikBengtsson/TopDom

The above information is also available as plain text as well as BibTeX entries via citation("TopDom").

Contributions

This Git repository uses the Git Flow branching model (the git flow extension is useful for this). The develop branch contains the latest contributions and other code that will appear in the next release, and the master branch contains the code of the latest release.

Contributing to this package is easy. Just send a pull request. When you send your PR, make sure develop is the destination branch on the TopDom repository. Your PR should pass R CMD check --as-cran, which will also be checked by Travis CI and AppVeyor CI when the PR is submitted.

Software status

Resource:	CRAN	Travis CI	AppVeyor
Platforms:	Multiple	Linux & macOS	Windows
R CMD check
Test coverage