News and Developments¶
April 3, 2017
- Added option to plot bigwig files as a line hicPlotTADs
- Updated documentation
- Improved hicPlotMatrix –region output
- Added compressed matrices. In our tests the compressed matrices are significantly smaller.
March 28, 2017
March 28, 2017
This release adds a quality control module to check the results from hicBuildMatrix. By default, now hicBuildMatrix generates a HTML page containing the plots from the QC measures. The results from several runs of hicBuildMatrix can be combined in one page using the new tool hicQC.
Also, this release added a module called hicCompareMatrices that takes two Hi-C matrices and computes the difference, the ratio or the log2 ratio. The resulting matrix can be plotted with hicPlotMatrix to visualize the changes.
Preprint introducing HiCExplorer is now online¶
March 8, 2017
Our #biorXiv preprint on DNA sequences behind Fly genome architecture is online!
Read the article here : http://biorxiv.org/content/early/2017/03/08/115063
In this article, we introduce HiCExplorer : Our easy to use tool for HiC data analysis, also available in Galaxy.
We also introduce HiCBrowser : A standalone software to visualize HiC along with other genomic datasets.
Based on HiCExplorer and HiCBrowser, we built a useful resource for anyone to browse and download the chromosome conformation datasets in Human, Mouse and Flies. It’s called the chorogenome navigator
Along with these resources, we present an analysis of DNA sequences behind 3D genome of Flies. Using high-resolution HiC analysis, we find a set of DNA motifs that characterize TAD boundaries in Flies and show the importance of these motifs in genome organization.
We hope that these resources and analysis would be useful for the community and welcome any feedback.