HiCExplorer addresses the common tasks of Hi-C data analysis from processing to visualization.
HiCExplorer is available as a command line suite of tools on this GitHub repository.
A Galaxy HiCExplorer version is directly available to users at http://hicexplorer.usegalaxy.eu. Training material is available at the Galaxy Training Network, while a Galaxy Tour is available here for users not familiar with this platform. Galaxy HiCExplorer is also available as a Docker image at the Docker Galaxy HiCExplorer GitHub repository. Finally, this Galaxy version is available on the Galaxy Tool Shed and on the corresponding GitHub repository.
| tool | description |
|---|---|
| :ref:`hicFindRestSite` | Identifies the genomic locations of restriction sites |
| :ref:`hicBuildMatrix` | Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads |
| :ref:`hicQuickQC` | Estimates the quality of Hi-C dataset |
| :ref:`hicQC` | Plots QC measures from the output of hicBuildMatrix |
| :ref:`hicCorrectMatrix` | Uses iterative correction to remove biases from a Hi-C matrix |
| :ref:`hicDetectLoops` | Identifies enriched Hi-C contacts |
| :ref:`hicCorrelate` | Computes and visualizes the correlation of Hi-C matrices |
| :ref:`hicFindTADs` | Identifies Topologically Associating Domains (TADs) |
| :ref:`hicMergeDomains` | Merges TADs of different resolutions |
| :ref:`hicDifferentialTAD` | Computes differential TADs between two Hi-C samples |
| :ref:`hicPCA` | Computes for A / B compartments the eigenvectors |
| :ref:`hicTransform` | Computes a obs_exp matrix like Lieberman-Aiden (2009), a pearson correlation matrix and or a covariance matrix. These matrices can be used for plotting. |
| :ref:`hicMergeMatrixBins` | Merges consecutive bins on a Hi-C matrix to reduce resolution |
| :ref:`hicMergeTADbins` | Uses a BED file of domains or TAD boundaries to merge the bin counts of a Hi-C matrix. |
| :ref:`hicPlotDistVsCounts` | Plot the decay in interaction frequency with distance |
| :ref:`hicPlotMatrix` | Plots a Hi-C matrix as a heatmap |
| :ref:`hicPlotTADs` | Plots TADs as a track that can be combined with other tracks (genes, signal, interactions) |
| :ref:`hicPlotViewpoint` | A plot with the interactions around a reference point or region. |
| :ref:`hicAggregateContacts` | A tool that allows plotting of aggregated Hi-C sub-matrices of a specified list of positions. |
| :ref:`hicSumMatrices` | Adds Hi-C matrices of the same size |
| :ref:`hicPlotDistVsCounts` | Plots distance vs. Hi-C counts of corrected data |
| :ref:`hicInfo` | Shows information about a Hi-C matrix file (no. of bins, bin length, sum, max, min, etc) |
| :ref:`hicCompareMatrices` | Computes difference or ratio between two matrices |
| :ref:`hicAverageRegions` | Computes the average of multiple given regions, usually TAD regions |
| :ref:`hicPlotAverageRegions` | visualization of hicAverageRegions |
| :ref:`hicNormalize` | Normalizes the given matrices to 0-1 range or the smallest read coverage |
| :ref:`hicConvertFormat` | Converts between different Hi-C interaction matrices |
| :ref:`hicAdjustMatrix` | Keeps, removes or masks regions in a Hi-C matrix |
| :ref:`hicValidateLocations` | Compare the loops with known peak protein locations |
| :ref:`hicMergeLoops` | Merges loops of different resolutions |
| :ref:`hicCompartmentalization` | Compute the global compartmentalization signal |
| :ref:`chicQualityControl` | Quality control for cHi-C data |
| :ref:`chicViewpointBackgroundModel` | Background model computation for cHi-C analysis |
| :ref:`chicViewpoint` | Computation of all viewpoints based on background model for cHi-C analysis |
| :ref:`chicSignificantInteractions` | Detection of significant interactions per viewpoint based on background model |
| :ref:`chicAggregateStatistic` | Compiling of target regions for two samples as input for differential analysis |
| :ref:`chicDifferentialTest` | Differential analysis of interactions of two samples |
| :ref:`chicPlotViewpoint` | Plotting of viewpoint with background model and highlighting of significant and differential regions |
| :ref:`hicPlotSVL` | Computing short vs long range contacts and plotting the results |
| :ref:`hicHyperoptDetectLoops` | Search for optimal hicDectectLoops parameters |
| :ref:`hicHyperoptDetectLoopsHiCCUPS` | Search for optimal Juicer HiCCUPS parameters |
- For all kind of questions, suggesting changes/enhancements and to report bugs, please create an issue on our GitHub repository
- In the past we offered to post on Biostars with Tag hicexplorer : Biostars or on the deepTools mailing list. We still check these resources from time to time but the preferred way to communicate are GitHub issues.
.. toctree:: :maxdepth: 2 content/installation content/list-of-tools content/example_usage content/News content/citation
Please cite HiCExplorer as follows:
Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning. Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization, Nucleic Acids Research, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W177–W184, https://doi.org/10.1093/nar/gkaa220
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
Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening,Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke. "High-resolution TADs reveal DNA sequences underlying genome organization in flies". Nature Communications, Volume 9, Article number: 189 (2018), doi: https://doi.org/10.1038/s41467-017-02525-w
This tool suite is developed by the Bioinformatics Unit at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg and by the Bioinformatics Lab of the Albert-Ludwigs-University Freiburg, Germany.