TopDom-data: Data for the TopDom Package

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

Data for the TopDom Package

Description

The ‘exdata/’ folder of this package provides a example data set used in examples. The data are also used to validate the TopDom implementation toward the original TopDom scripts.

Origin

The data herein contain a tiny subset of the HiC and TopDom data used in the TopDom study (Shin et al., 2016). More precisely, it contains:

1. A TopDom file ‘mESC_5w_chr19.nij.HindIII.comb.40kb.domain’, which is part of the ‘mESC_5w_domain.zip’ file (5,504 bytes; md5 ffb19996f681a4d35d5c9944f2c44343) from the Supplementary Materials of Shin et al. (2016). These data were downloaded from the TopDom website (http://zhoulab.usc.edu/TopDom/ - now defunct).

2. A normalized HiC-count matrix file ‘nij.chr19.gz’, where the non-compressed version is part of the ‘mESC.norm.tar.gz’ file (1,305,763,679 bytes; md5 2e79d0f57463b5b7c4bf86b187086d3c) made available by UCSD Ren Lab originally downloaded from ‘http://chromosome.sdsc.edu/mouse/hi-c/download.html’ (no longer available). 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).

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.

HenrikBengtsson/TopDom documentation built on April 9, 2023, 2:11 a.m.