README.md

In HenrikBengtsson/TopDomStudy: TopDom Study by Segal et al.

TopDomStudy: TopDom Study by Segal et al.

Requirements

This R package depends on several R packages. Most of them are available on CRAN but not all. Currently, the following package is available only on GitHub:

• GSE84920.parser - Parsers for the GSE84920 Hi-C Data Sets of Ramani et al. (2017)

However, you do not need to install those manually as long as you follow the installation instruction below; they will be install automatically.

Moreover, this packages produces and makes use of pathnames that are longer than 255 characters. Unfortunately, this means that this package does not run on MS Windows (https://github.com/HenrikBengtsson/TopDomStudy/issues/3). The package tests have been validated on Linux and macOS.

References

1. Ramani, V., Deng, X., Qiu, R., Gunderson, K. L., Steemers, F. J., Disteche, C. M., ..., Shendure, J. (2017). Massively multiplex single-cell Hi-C. Nature methods, 14(3), 263–266. doi:10.1038/nmeth.4155, PMC5330809.

2. Shin, et al., TopDom: an efficient and deterministic method for identifying topological domains in genomes, Nucleic Acids Res. 2016 Apr 20; 44(7): e70., 2016. doi: 10.1093/nar/gkv1505, PMCID: PMC4838359, PMID: 26704975.

Installation

R package TopDomStudy is only available via GitHub and can be installed in R as:

remotes::install_github("HenrikBengtsson/TopDomStudy", ref="master")

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use:

remotes::install_github("HenrikBengtsson/TopDomStudy", ref="develop")

This will install the package from source.

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 TopDomStudy 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: | GitHub | Travis CI | AppVeyor | | ------------- | ------------------- | --------------- | ---------------- | | Platforms: | Multiple | Linux & macOS | Windows | | R CMD check | | | | | Test coverage | | | |

HenrikBengtsson/TopDomStudy documentation built on May 14, 2021, 1:49 p.m.