HiCExplorer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HiCExplorer

Tool usage distribution map

This map represents all the scientific publications referring to HiCExplorer per scientific context
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Associated diseases


Popular tool citations

chevron_left Topologically domain calling Normalization Bioinformatics workflows Heatmap generation Contact matrix generation chevron_right
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HiCExplorer specifications


Unique identifier OMICS_16745
Name HiCExplorer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Thomas Manke

Publications for HiCExplorer

HiCExplorer citations


Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

Nat Commun
PMCID: 5786002
PMID: 29374152
DOI: 10.1038/s41467-017-02762-z

[…] o perform a de novo motif analysis using the “size given” option. GREAT was used to identify genes in proximity (≤10 kb) to LMRs and to annotate genes within regulatory domains of SNPs. DeepTools and HiCExplorer were used to display traces and heatmaps and to perform cluster analysis. Annotations and genome files (hg19) were obtained from the UCSC. Prism 5 (GraphPad) was used for statistical analy […]


High resolution TADs reveal DNA sequences underlying genome organization in flies

Nat Commun
PMCID: 5768762
PMID: 29335486
DOI: 10.1038/s41467-017-02525-w

[…] e visualizations of Hi-C data that can integrate other data sources, examples of which can be seen throughout this manuscript. Further information can be found at the associated documentation (http://hicexplorer.readthedocs.io), which includes a full analysis workflow and detailed description of the tools.Fig. 6Our tools would be beneficial to users that do not routinely perform expensive and tech […]


Chromatin associated RNA sequencing (ChAR seq) maps genome wide RNA to DNA contacts

PMCID: 5962340
PMID: 29648534
DOI: 10.7554/eLife.27024.037

[…] ced using 2 × 75 paired end reads and were aligned to blacklisted and repeatmasked genome using the ‘local’ and ‘reorder’ flags. The subsequent bam files were used to build the contact matrices using HiCExplorer (https://github.com/deeptools/HiCExplorer/blob/master/docs/index.rst). Matrices were built at 10 kb resolution. Data from GEO:GSE58821 were downloaded, re-aligned and processed using HiCEx […]


DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes

Nat Commun
PMCID: 5698409
PMID: 29162810
DOI: 10.1038/s41467-017-01724-9

[…] s were mapped as single-end reads to the reference genome mm9 with Bowtie2 using the local alignment mode (--local). Then, properly mapped reads were sorted by their read names (-n) with SAMtools.The HiCExplorer (version 1.7.2, https://github.com/maxplanck-ie/HiCExplorer) was used for processing of mapped reads, normalizing, analyzing, and visualization of Hi-C data.Using mapped and sorted reads, […]

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HiCExplorer institution(s)
Max Planck Institute of Immunobiology and Epigenetics, Bioinformatics Unit, Freiburg, Germany; Max Planck Institute of Biochemistry, Computational Biology, Martinsried, Germany; Max Planck Institute of Immunobiology and Epigenetics, Sequencing Facility, Freiburg, Germany; University of Freiburg, Department of Computer Science, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
HiCExplorer funding source(s)
This work was supported by the German Research Foundation [SFB 992, Project Z01] and a grant from the Federal Ministry of Education and Research through the German Epigenome Programme DEEP [01KU1216G].

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