HiCExplorer¶
Set of programs to process, normalize, analyze and visualize Hi-C data¶
HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization.
The following is the list of tools available in HiCExplorer¶
| tool | description |
|---|---|
| findRestSites | Identifies the genomic locations of restriction sites |
| hicBuildMatrix | Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads |
| hicQC | Plots QC measures from the output of hicBuildMatrix |
| hicCorrectMatrix | Uses iterative correction to remove biases from a Hi-C matrix |
| hicFindEnrichedContacts | Identifies enriched Hi-C contacts |
| hicCorrelate | Computes and visualises the correlation of Hi-C matrices |
| hicFindTADs | Identifies Topologically Associating Domains (TADs) |
| hicPCA | Computes for A / B compartments the eigenvectors |
| 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. |
| hicMergeMatrixBins | Merges consecutive bins on a Hi-C matrix to reduce resolution |
| hicMergeTADbins | Uses a BED file of domains or TAD boundaries to merge the bin counts of a Hi-C matrix. |
| hicPlotDistVsCounts | Plot the decay in interaction frequency with distance |
| hicPlotMatrix | Plots a Hi-C matrix as a heatmap |
| hicPlotTADs | Plots TADs as a track that can be combined with other tracks (genes, signal, interactions) |
| hicPlotViewpoint | A plot with the interactions around a reference point or region. |
| hicAggreagteContacts | A tool that allows plotting of aggregated Hi-C sub-matrices of a specified list of positions. |
| hicSumMatrices | Adds Hi-C matrices of the same size |
| hicPlotDistVsCounts | Plots distance vs. Hi-C counts of corrected data |
| hicExport | Export matrix to text formats |
| hicInfo | Shows information about a Hi-C matrix file (no. of bins, bin length, sum, max, min, etc) |
| hicCompareMatrices | Computes difference or ratio between two matrices |
| hicLog2Ratio | Computes the log2 ratio between two matrices. |
Getting Help¶
- 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
Citation¶
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”. 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.