HenrikBengtsson / TopDomData

R package: TopDomData - Data for the TopDom Package

TopDomData - Data for the TopDom Package

The TopDomData package is an R package that provides examples data for the TopDom package. This data package is also used for validation of implementation of the TopDom package via TopDom's package tests.

The data in this package contain a tiny subset of the HiC and TopDom data used in the TopDom study (Shin et al., 2016). More precisely, folder system.file("exdata", package="TopDomData") contains:

1. A TopDom file mESC_5w_chr10.nij.HindIII.comb.40kb.domain, which is part of the mESC_5w_domain.zip file (54,676 bytes; md5 1ebfb9a556c1954b8cd35520a2499abd) from the Supplementary Materials of Shin et al. (2015). These data were downloaded from the TopDom website (http://zhoulab.usc.edu/TopDom/ - now defunct).

2. A normalized 3250-by-3250 HiC-count matrix file nij.chr10.gz, where the non-compressed version is part of the mESC.norm.tar.gz file (1,305,763,679 bytes; md5 2e79d0f57463b5b7c4bf86b187086d3c) originally downloaded from the UCSD Ren Lab. It is a tab-delimited file containing a 3250-by-3250 numeric matrix non-negative decimal values. The underlying HiC sequence data is available from GSE35156 on GEO and was published part of Dixon, et al. (2012).

For full details, please see help("TopDomData", package="TopDomData").

References

1. Dixon JR, Selvaraj S, Yue F, Kim A, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012 Apr 11; 485(7398):376-80, doi: 10.1038/nature11082, PMCID: PMC3356448, PMID: 22495300.

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

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

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

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 TopDomData 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