News and Developments¶
3 April 2019
Python 3 only. Python 2.X is no longer supported
Additional Hi-C interaction matrix correction algorithm ‘Knight-Ruiz’ as a C++ module for a faster runtime and less memory usage.
Enriched regions detection tool: ‘hicDetectLoops’ based on strict candidate selection, ‘hicFindEnrichedContacts’ was deleted
Metadata for cooler files is supported: hicBuildMatrix and hicInfo are using it
New options for hicPlotMatrix: –loops to visualize computed loops from hicDetectLoops and –bigwigAdditionalVerticalAxis to display a bigwig track on the vertical axis too.
22 March 2019
This bug fix release patches an issue with cooler files, hicBuildMatrix and the usage of a restriction sequence file instead of fixed bin size.
27 February 2019
This bug fix release removes reference to hicExport that were forgotten to delete in 2.2. Thanks @BioGeek for this contribution.
7 February 2019
Muting log output of matplotlib and cooler
Set version number of hicmatrix to 7
Optional parameter for hicInfo to write the result to a file instead to the bash
18 January 2019
This release contains:
replaced hicExport by hicConvertFormat and hicAdjustMatrix
extended functionality for hicConvertFormat
read support for homer, hicpro, cool, h5
write support for h5, homer, cool
convert hic to cool
creation of mcool matrices
remove, keep or mask specified regions from a file, or chromosomes
normalize matrices to 0 - 1 range or to the read coverage of the lowest given
support for build mcool
restructuring the central class HiCMatrix to object oriented model and moved to its own library: deeptools/HiCMatrix.
Extended read / write support for file formats
better (faster, less memory) support for cool format
remove of old, unused code
restrict support to h5 and cool matrices, except hicConvertFormat
hicFindTADs: Option to run computation per specified chromosomes
hicPlotTADs: removed code and calls pyGenomeTracks
hicAverageRegions: Sum up in a given range around defined reference points. Useful to detect changes in TAD structures between different samples.
hicPlotAverageRegions: Plots such a average region
hicTransform: Restructuring the source code, remove of option ‘all’ because it was generating confusion. Adding option ‘exp_obs’, exp_obs_norm and exp_obs_lieberman. These three different options use different expectation matrix computations.
Adding –norm option to compute the expected matrix in the way HOMER is doing it. Useful for drosophila genomes
Adding option to write out the intermediate matrices ‘obs_exp’ and ‘pearson’ which are necessary in the computation of the PCA
Add option to clip bigwig values
Add option to scale bigwig values
Removed hicLog2Ration, functionality is covered by hicCompareMatrices
Extending test cases to cover more source code and be hopefully more stable.
Many small bugfixes
13 June 2018
We are proud to announce our latest publication:
Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A Grüning. “Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization”, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi: https://doi.org/10.1093/nar/gky504
25 May 2018
cooler file format correction factors are applied as they should be
parameter ‘–region’ of hicBuildMatrix works with Python 3
7 May 2018
The third bugfix release of version 2.1 corrects an error in hicPlotViewpoint. It adds a feature requested in issue #169 which should have been included in release 2.1 but was accidentally not.
From 2.1 release note: hicPlotViewpoint: Adds a feature to plot multiple matrices in one image
26 April 2018
The second bug fix release of 2.1 includes:
fixing broken Readthedocs documentation
Small bug fix concerning hicPlotMatrix and cooler: –chromosomeOrder is now possible with more than one chromosome
Small fixes concerning updated dependencies: Fixing version number a bit more specific and not that strict in test cases delta values.
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 Gina Renschler and Gautier Richard from the MPI-IE Freiburg, Germany.
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
bug fixes for
--perChroption in hicPlotMatrix
eigenvector track with
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
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.