News and Developments¶
10 November 2020
- hicAggregateContacts, thanks @LeilyR:
hicAggragateContact has been updated to be able to handle inter chromosomal contacts as well as inter chromosomal contacts
Added scikit-learn to dependencies
hicBuildMatrix: Fixing another bug concerning scaffolds without any restriction enzyme cut site
Adding default values to the documentation. Thanks @lldelisle
hicTransform: Fixing a bug in case one of the intermediate matrices is empty
- Official Python 3.8 support:
Manually setting ‘fork’ as the start method for multiprocessing because the default on macOS was set to ‘spawn’
14 October 2020
- Bug fix release:
Reads from scaffolds without any restriction enzyme cut site are considered as ‘same fragment’. An appearance of such a read will not lead to a crash anymore
Minor documentation improvements
06 October 2020
- Bug fix release:
enforcing version 15 of HiCMatrix. Version 14 had a bug concerning the application of the correction factors of cool files. See issue #595
Fixing a bug in hicDetectLoops in single-core mode. Thanks @alecw
Fixing a bug in hicDifferentialTAD concerning multiple chromosomes in the bed file. See issue #587
Updating dependencies to newest versions, except biopython. Forcing here <1.77 because their API change is breaking our source code. See issue #609
Changing internal structure of the docs. Navigation should be better now.
11 August 2020
hicBuildMatrix: Better help text
patch for hicPlotMatrix if matrix does not start at 0 and –region is used
bug fix for remove option in hicAdjustMatrix
10 July 2020
Major update for hicDetectLoops: Results are now closer to HiCCUPS, it is faster and needs less memory.
hicHyperoptDetectLoops: New tool to compute the best parameter setting if the number of expected loops is given and a protein boundary file (e.g. CTCF on mammals) is provided
hicHyperoptDetectLoopsHiCCUPS: New tool to compute the best parameter setting for Juicers HiCCUPS. HiCCUPS and all its dependencies are not part of HiCExplorer and must be provided by the user. Number of expected loops and a protein boundary file (e.g. CTCF on mammals) must be provided.
hicMergeDomains: New tool to compute a merge of TADs computed on different resolutions. Moreover it provides a cleaning of the boundaries with the help of a protein peak file, and the hierarchical dependencies of TADs can be plotted. This tool is the result of the Bachelor thesis from Sarah Domogalla (@SarahMaria27). Thanks for your contribution!
hicDifferentialTAD: New tool to compute differential TADs between two samples
Bug fix for hicFindTADs: The format of the intermediate z-score matrices are now depending on the format of the input Hi-C matrix
Bug fix for chic*-modules: Fixate range is now correct applied.
chicSignificantInteractions, hicDetectLoops: Option to use a per relative position p-value with a p-value threshold file
Adding hicCreateThresholdFile: A script to generate a per position p-value threshold for hicDetectLoops and chicSignificantInteractions
- Bug fix for hicPlotMatrix:
multiple bigwig tracks in the vertical setting are now supported
correct plot of bigwig if the given matrix does not start at the beginning of the chromosome
new parameters ‘increaseFigureWidth’ and ‘increaseFigureHeight’ to add more space to the plot if multiple bigwigs are plotted. Adjust this parameter to correct the plot of the heatmap which may be not quadratic anymore.
restriction of the loop regions to the user given range. This effects especially SVGs that will now contain less objects as before.
- New feature for hicBuildMatrix:
multiple restriction cut sequences, dangling ends and restriction cut sites files are now supported
restriction cut sequences, dangling ends and restriction cut sites files are now mandatory parameters. This is now enforced to guarantee a correct detection of self ligations and self circles
hicPrepareQCreport: New support for multiple dangling ends
hicQuickQC: restriction cut sequences, dangling ends and restriction cut sites files are now mandatory parameters
hicFindRestSite: gz support for fasta file
Add fallback modes to multiple scripts if the parallelization fails.
hicAggregate: interactions between two bed files by comparing every row in the first bed file with its corresponding row in the second file. (issue #390)
- hicAdjustMatrix: fix #341, 454
fixed –action remove: it actually remove the part from the matrix previously was masking it
the case where the end of the chromosome need to be removed.
New Azure testing for the general test cases, the trivial ones run on travis
02 July 2020
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W177–W184
23 March 2020
Fixing the wrong p-value computation in for chicViewpoint. New method is more accurate for floating points.
Fixing a bug in chicViewpointBackgroundModel and chicQualityControl if an non-existing reference point was used.
Improving all chic* modules with a capturing of errors in sub-processes. It is now guaranteed that the computation will terminate. Either successful or by error.
Add option ‘truncateZero’ to chicViewpointBackgroundModel: This removes all zero values for the distributions before fitting to fight over dispersion.
Add option ‘decimalPlaces’ to chicViewpoint to adjust the decimal places in the output for all floating values. Helpful for really small p-values
Add option ‘truncateZeroPvalues’ to chicSignificantInteractions to set all p-values which are 0 to 1 and are therefore ignored.
Add option ‘truncateZeroPvalues’ to chicPlotViewpoint to set all p-values which are 0 to 1 and do not disturb the presentation of real p-values
7 March 2020
This release fixes the wrong name scheme which was used in the chicModules. The most .bed files are now .txt files.
hicDetectLoops got an inner chromosome parallelization to decrease the compute time.
hicPlotMatrix got three new parameters: rotationX, rotationY and fontSize to adjust the position and font size of the labels. We hope this can lead in certain cases to a a better readability
hicPlotMatrix: fixed a bug that occurred if the list of chromosomes was given and the last chromosome appeared as an additional label.
Improving and updating the documentation.
**6 March 2020*
The preprint of the loop detection algorithm is online via biorXiv: https://www.biorxiv.org/content/10.1101/2020.03.05.979096v1
3 February 2020
This release fixes a bug in chicViewpoint that caused a crash if the data to be averaged is less than the window size.
28 January 2020
Fixing a bug in hicAdjustMatrix: keep option had a bug concerning the cutting before the end of a chromosome or the start position was not from the beginning of the chromosome
hicCompartmentPolarization was renamed to hicCompartmentalization and got some bug fixes
Extending the option on how the observed vs. Expected matrix is computed and adding the parameter –ligation_factor to achieve a rescale behaviour of the values as it is implemented in Homer. The same changes are applied to hicTransform
Improved the documentation
Adding an option in hicAverageRegions to select start, end, center or start_end as start index for up/downstream range.
hicBuildMatrix: Removed default value of binSize to enable mutually exclusive group error if not one of them is set. Behaviour so far was that the binSize was taken.
hicPlotSVL: adding xlegend to plot of SVL ratios to indicate the data points per boxplots are the chromosome ratios
hicQuickQC: Removed binSize option of hicQuickQC because it does not matter for QC calculation and adding a sentence to recommend the usage of restriction enzyme and dangling end sequence. Fixing bug issue #464
hicNormalize: Adding option in hicNormalize to remove values after the normalization if values are smaller than a given threshold
Capture Hi-C modules: Change background model distribution assumption from negative binomial to continuous negative binomial by using Gamma functions as a replacement for the binomial coefficient. Source: https://stats.stackexchange.com/questions/310676/continuous-generalization-of-the-negative-binomial-distribution/311927
hicInfo: Implementing feature request #456. The length of chromosomes is now show in the information too
15 November 2019
Fixing a bug in the labeling of chicPlotViewpoints if the value range is counted in MB
Add an option to chicViewpoint to pre-compute a x-fold of p-value over the maximum value of the relative distance
8 October 2019
- Fixing many bugs:
A bug in hicDetectLoops if a sub-matrix was very small
A bug in hicPlotMatrix if the region defined by –region was only a chromosome and loops should be plotted too
A bug in hicPlotMatrix if a loop region should be plotted and chromosomeOrder argument was used too
A bug in hicAggregateContacts (issue #405) if chromosomes were present in the matrix but not in the bed file
A bug in hicAdjustMatrix concerning a bed file and consecutive regions, see issue #343
A bug in hicAdjustMatrix if a chromosome is present in the matrix but not in the bed file, see issue #397
A bug in hicCompartmentsPolarization concerning the arguments ‘quantile’ and ‘outliers’ were interpreted as strings but should be integers
A bug in hicAdjustMatrix concerning the ‘keep’ option and how matrices are reordered internally. Thanks @LeilyR
- Added features as requested:
hicPCA ignores now masked bins, see issue #342
Better legend handling on x-axis
Peaks are now display with their fill width
Add option –pValueSignificantLevels to categorize the p-values in x levels (e.g. 0.001 0.05 0.1)
adding sorting via viewpoints and not by samples option (–allViewpointsList)
Adding an option to hicNormalize to normalize via multiplication and a use defined value (see issues #385, #424)
Rearrange hicAdjustMatrix to have a better accessibility to its functions from outside of main
Improving the documentation and fixing grammar / spelling mistakes. Thanks @simonbray
New script: hicPlotSVL to investigate short range vs long range ratios.
** 22 August 2019**
Adding the new captured Hi-C module. Viewpoint analysis based on a background model, significant interaction detection and differential analysis are provided.
Adding documentation for captured Hi-C module and a tutorial on how to use it.
Adding a module to be able to detect quite fast the quality of a Hi-C data set: hicQuickQC.
Adding a tool to merge loops of different resolutions.
Improving validation of locations: Presorting is no longer necessary; adding feature to add ‘chr’ prefix to loop or protein chromosome name
- Change loop detection slightly to improve results and fixed bugs:
preselection p-value was ignored and only p-value was used
adding additional test to the peak region test to decrease false discoveries
exchanging pThreshold / ln(distance) to remove too low values by a share of the maximum value of the distance. New parameter ‘maximumInteractionPercentageThreshold’
Removal of the folder ‘scripts’ and its content. These were outdated scripts and will maybe part of regular Hi-C tools in the future.
9 July 2019
KR correction improvements: It is now able to process larger data sets like GM12878 primary+replicate on 10kb resolution.
Adding script for validation of loop locations with protein peak locations
Adding script hicCompartmentsPolarization: Rearrange the average interaction frequencies using the first PC values to represent the global compartmentalization signal
28 June 2019
Pinning dependencies to:
hicmatrix version 9: API changes in version 10
krbalancing version 0.0.4: API changes in version 0.0.5
matplotlib version 3.0: Version 3.1 raises ‘Not implemented error’ for unknown reasons.
Set fit_nbinom to version 1.1: Version 1.0 Had deprecated function call of scipy > 1.2.
Small documentation fixes and improvements.
5 April 2019
Fixes KR balancing correction factors
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.