News and Developments¶
27 March 2018
This release fixes a problem related to python3 in which chromosome names were of bytes type
5 March 2018
The 2.1 version of HiCExplorer comes with new features and bugfixes.
- Adding the new feature hicAggregateContacts: A tool that allows plotting of aggregated Hi-C sub-matrices of a specified list of positions.
- Many improvements to the documentation and the help text. Thanks to @GinaRe and @gtrichard.
- supports only bigwig files for an additional data track.
- the argument –pca was renamed to –bigwig
- Smoothing the bigwig values to neighboring bins if no data is present there
- Fixes to a bug concerning a crash of tight_layout
- Adding the possibility to flip the sign of the values of the bigwig track
- Adding the possibility to scale the values of the bigwig track
- hicPlotViewpoint: Adds a feature to plot multiple matrices in one image
- cooler file format:
- supports mcool files
- applies correction factors if present
- optionally reads bin[‘weight’]
- a crash in hicPlotTads if horizontal lines were used
- checks if all characters of a title are ASCII. If not they are converted to the closest looking one.
- Updated and fixate version number of the dependencies
December 21, 2017
This release makes HiCExplorer ready for the future:
- Python 3 support
- Cooler file format support
- A/B comparment analysis
- Improved visualizations
- bug fixes for –perChr option in hicPlotMatrix
- eigenvector track with –pca for hicPlotMatrix
- visualization of interactions around a reference point or region with hicPlotViewpoint
- Higher test coverage
- re-licensing from GPLv2 to GPLv3
November 27, 2017
Bug fix release:
- a fix concerning the handling chimeric alignments in hicBuildMatrix. Thanks to Aleksander Jankowski @ajank
- handling of dangling ends was too strict
- improved help message in hicBuildMatrix
October 25, 2017
This release is adding new features and fixes many bugs:
- hicBuildMatrix: Added multicore support, new parameters –threads and –inputBufferSize
- One call instead of two: hicFindTADs TAD_score and hicFindTADs find_TADs merged to hicFindTADs.
- New multiple correction method supported: False discovery rate. Call it with –correctForMultipleTesting fdr and –threshold 0.05.
- Update of the tutorial: mES-HiC analysis.
- Additional test cases and docstrings to improve the software quality
- Fixed a bug occurring with bigwig files with frequent NaN values which resulted in only NaN averages
- hicPlotTADs: Support for plotting points
- Moved galaxy wrappers to https://github.com/galaxyproject/tools-iuc
- Fixed multiple bugs with saving matrices
- hicCorrelate: Changes direction of dendograms to left
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 Hi-C data analysis, also available in Galaxy.
We also introduce HiCBrowser : A standalone software to visualize Hi-C 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 Hi-C 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.