tools/hicFindRestSite tools/hicBuildMatrix tools/hicSumMatrices tools/hicMergeMatrixBins tools/hicCorrectMatrix tools/hicNormalize
tools/hicQuickQC tools/hicQC tools/hicCorrelate tools/hicPlotDistVsCounts tools/hicInfo
tools/hicCompareMatrices tools/hicPCA tools/hicTransform tools/hicAverageRegions tools/hicDetectLoops tools/hicValidateLocations tools/hicMergeLoops tools/hicHyperoptDetectLoops tools/hicHyperoptDetectLoopsHiCCUPS tools/hicCompartmentalization tools/hicPlotSVL
tools/hicFindTADs tools/hicMergeDomains tools/hicDifferentialTAD tools/hicMergeTADbins tools/hicInterIntraTAD tools/hicTrainTADClassifier tools/hicTADClassifier
tools/hicPlotMatrix tools/hicPlotTADs tools/hicPlotViewpoint tools/hicAggregateContacts tools/hicPlotAverageRegions
tools/hicConvertFormat tools/hicAdjustMatrix
tools/chicQualityControl tools/chicViewpointBackgroundModel tools/chicViewpoint tools/chicSignificantInteractions tools/chicAggregateStatistic tools/chicDifferentialTest tools/chicPlotViewpoint
For single-cell Hi-C data analysis please use scHiCExplorer .
| tool | type | input files | main output file(s) | application |
|---|---|---|---|---|
hicFindRestSite |
preprocessing | 1 genome FASTA file | bed file with restriction site coordinates | Identifies the genomic locations of restriction sites |
hicBuildMatrix |
preprocessing | 2 BAM/SAM files | hicMatrix object | Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads |
hicCorrectMatrix |
preprocessing | hicMatrix object | normalized hicMatrix object | Uses iterative correction or Knight-Ruiz to remove biases from a Hi-C matrix |
hicMergeMatrixBins |
preprocessing | hicMatrix object | hicMatrix object | Merges consecutive bins on a Hi-C matrix to reduce resolution |
hicSumMatrices |
preprocessing | 2 or more hicMatrix objects | hicMatrix object | Adds Hi-C matrices of the same size |
hicNormalize |
preprocessing | multiple Hi-C matrices | multiple Hi-C matrices | Normalize data to 0 to 1 range or to smallest total read count |
hicCorrelate |
analysis | 2 or more hicMatrix objects | a heatmap/scatter plot | Computes and visualizes the correlation of Hi-C matrices |
hicFindTADs |
analysis | hicMatrix object | bedGraph file (TAD score), a boundaries.bed file, a domains.bed file (TADs) | Identifies Topologically Associating Domains (TADs) |
hicMergeDomains |
analysis | multiple TAD domain files | tad domain file with merged tad locations multiple files with plotted TAD relations | Merges detect TADs locations of different resolutions; hierarchical relation between TADs as multiple plots |
hicDifferentialTAD |
analysis | two Hi-C matrices one TAD domain file | two diff_tad files: accepted H0 and rejected H0. Similar to BED6 | Identifies differential Topologically Associating Domains (TADs) between two Hi-C matrices |
hicInterIntraTAD |
analysis | Hi-C matrix, TAD boundaries | data file and a plot | Computes and extracts TAD data. Creates a plot for the inter/intra contact ratio. |
hicTrainTADClassifier |
analysis | Hi-C matrix, TAD boundaries | ML model for hicTADClassifier | Computes a ML model for hicTADClassifier. |
hicTADClassifier |
analysis | Hi-C matrix, (ML model) | predicted TAD boundaries | Computes TAD boundaries based on a ML model from hicTrainTADClassifier |
hicPlotMatrix |
visualization | hicMatrix object | a heatmap of Hi-C contacts | Plots a Hi-C matrix as a heatmap |
hicPlotTADs |
visualization | hicMatrix object, a config file | Hi-C contacts on a given region, along with other provided signal (bigWig) or regions (bed) file | Plots TADs as a track that can be combined with other tracks (genes, signal, interactions) |
hicPlotDistVsCounts |
visualization | hicMatrix object | log log plot of Hi-C contacts per distance | Quality control |
hicConvertFormat |
data integration | one/multiple Hi-C file formats | Hi-C matrices/outputs in several formats | Convert matrix to different formats |
hicAdjustMatrix |
data integration | one Hi-C file formats | Hi-C matrix | Removes, masks or keeps specified regions of a matrix |
hicInfo |
information | one or more hicMatrix objects | Screen info | Prints information about matrices, like size, maximum, minimum, bin size, etc. |
hicPCA |
analysis | one Hi-C matrix | bedgraph or bigwig file(s) for each eigenvector | Computes for A / B compartments the eigenvectors |
hicTransform |
analysis | one Hi-C matrix | Hi-C matrix | 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. |
hicPlotViewpoint |
visualization | one Hi-C matrix | A viewpoint plot | A plot with the interactions around a reference point or region. |
hicQC |
information | log files from hicBuildMatrix | A quality control report | Quality control of the created contact matrix. |
hicQuickQC |
information | 2 BAM/SAM files | An estimated quality control report | Estimated quality report of the Hi-C data. |
hicCompareMatrices |
analysis | two Hi-C matrices | one Hi-C matrix | Applies diff, ratio or log2ratio on matrices to compare them. |
hicAverageRegions |
analysis | multiple Hi-C matrices | one npz object | Averages the given locations. Visualization with hicPlotAverageRegions |
hicDetectLoops |
analysis | one Hi-C matrices | bedgraph file with loop locations | Detects enriched regions. Visualization with hicPlotmatrix and --loop parameter. |
hicValidateLocations |
analysis | one loop, one protein peak file | bedgraph file with matched loop locations, one file with loop / protein statistics | Matches loop locations with protein peak positions |
hicMergeLoops |
analysis | multiple loop files | bedgraph file with merged loop locations | Merges detect loop locations of different resolutions |
hicHyperoptDetectLoops |
analysis | one Hi-C matrix, protein peaks | best parameter setting | Search for best parameter setting for hicDetectLoops |
hicHyperoptDetectLoopsHiCCUPS |
analysis | one Hi-C matrix, protein peaks | best parameter setting | Search for best parameter setting for Juicer's HiCCUPS |
hicCompartmentalization |
visualization | one Hi-C interaction matrix one PCA bedgraph file | one image polarization plot | The global compartmentalization signal. |
hicPlotAverageRegions |
visualization | one npz file | one image | Visualization of hicAverageRegions. |
hicPlotSVL |
analysis | one / multiple Hi-C matrices | one image, p-values file, raw data file | Computes short/long range contacts; a box plot, a p-value and raw data file |
hicMergeTADbins |
preprocessing | one Hi-C matrix, one BED file | one Hi-C matrix | Uses a BED file of domains or TAD boundaries to merge the bin counts of a Hi-C matrix. |
chicQualityControl |
preprocessing | Hi-C matrices reference point BED file | two plots accepted reference point BED file | Checks for sparsity of viewpoints and removes them if too sparse. |
chicViewpointBackgroundModel |
preprocessing | Hi-C matrices reference point BED file | background model file | Creates a background model for all given samples and reference points. |
chicViewpoint |
preprocessing | Hi-C matrices background model file | viewpoint file(s) | Creates per sample per viewpoint one viewpoint file. |
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chicDifferentialTest |
analysis | aggregated file(s) of two samples | H0_accepted-, H0_rejected-files | Tests with chi2 or fisher for differential interactions of two samples. |
chicPlotViewpoint |
visualization | viewpoint file(s) differential expression file(s) significant interactions file(s) | one image per viewpoint | Visualization of a viewpoint. |
A typical HiCExplorer command could look like this:
$ hicPlotMatrix -m myHiCmatrix.h5 \
-o myHiCmatrix.pdf \
--clearMaskedBins \
--region chrX:10,000,000-15,000,000 \
--vMin -4 --vMax 4 \You can always see all available command-line options via --help:
$ hicPlotMatrix --help- Output format of plots should be indicated by the file ending, e.g.
MyPlot.pdfwill return a pdf file,MyPlot.pnga png-file. - Most of the tools that produce plots can also output the underlying data - this can be useful in cases where you don't like the HiCExplorer visualization, as you can then use the data matrices produced by deepTools with your favorite plotting tool, such as R.
- The vast majority of command line options are also available in Galaxy (in a few cases with minor changes to their naming).