HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization.
| tool | description |
|---|---|
| :ref:`findRestSites` | 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:`hicCorrectMatrix` | Uses iterative correction to remove biases from a Hi-C matrix |
| :ref:`hicFindEnrichedContacts` | Identifies enriched Hi-C contacts |
| :ref:`hicCorrelate` | Computes and visualises the correlation of Hi-C matrices |
| :ref:`hicFindTADs` | Identifies Topologically Associating Domains (TADs) |
| :ref:`hicMergeMatrixBins` | Merges consecutives bins on a Hi-C matrix to reduce resolution |
| :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:`hicSumMatrices` | Adds Hi-C matrices of the same size |
| :ref:`hicPlotDistVsCounts` | Plots distance vs. Hi-C counts of corrected data |
| :ref:`hicExport` | Export matrix to text formats |
- For general questions, please use Biostars with Tag hicexplorer : Biostars
- For specific questions and feature requests, use the deepTools mailing list
- For suggesting changes/enhancements and to report bugs, please create an issue on our GitHub repository
.. toctree:: :maxdepth: 2 content/installation content/list-of-tools content/example_usage content/News
Please cite HiCExplorer as follows:
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". bioRxiv 115063 doi: https://doi.org/10.1101/115063
This tool suite is developed by the Bioinformatics Unit at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.