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The TopDom method identifies topological domains in genomes from Hi-C sequence data (Shin et al., 2016). 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.
Whenever using the TopDom method, please cite:
Whenever using the TopDom package, please cite:
The above information is also available as plain text as well as
BibTeX entries via citation("TopDom").
Please note that I, Henrik Bengtsson, is not the developer
of the TopDom method (Shin et al. 2016), or the (original) TopDom code
available from the TopDom authors. As I needed the TopDom method in a
project, I ended up putting their TopDom_v0.0.*.R scripts
into a proper R package (this TopDom package) so I
could validate the[ir] code via R CMD check and so on. Then
I started to add a bit of help documentation to make my own life easier.
I also found a few bugs that I fixed and did some improvements but I
really tried not to diverge from the original functionality.
Now, since I find it a waste of resources if someone else has to go through the same efforts that I had to, I decided to make this package public. The goal is also to submit the TopDom package to CRAN so that the TopDom method is properly archived for reproducible purposes. In order to do this, the original authors agreed on releasing their original TopDom scripts under the GPL license, which is also the license of the TopDom package.
Having said this, please note that I don’t intend to do user support for the TopDom method, how to use it, add new features, and so on. This is simply because I don’t have the resources to do that. More importantly, I am not the best person to answer questions on the TopDom method and its implementation. Instead, I recommend that you reach out to the original TopDom authors to get your questions answered.
The original R script (versions 0.0.1 and 0.0.2) and the TopDom manual were made available on a website of the TopDom author (http://zhoulab.usc.edu/TopDom/). As of 2019, that website is no longer available. Instead, TopDom is now listed as a paragraph on https://labs.dgsom.ucla.edu/zhou/pages/software with a link to one of the author GitHub repository jasminezhoulab/TopDom, which holds the TopDom manual and version 0.0.2 of the script but not version 0.0.1.
R package TopDom is only available via GitHub and can be installed in R as:
remotes::install_github("HenrikBengtsson/TopDom", ref="master")To install the pre-release version that is available in Git branch
develop on GitHub, use:
remotes::install_github("HenrikBengtsson/TopDom", ref="develop")This will install the package from source.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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