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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



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  • person_outline Thomas Manke <>

Publications for HiCExplorer

HiCExplorer in publications

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

[…] 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 […]

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

[…] an abundance of new studies about topologically associating domains (tads), the role of genetic information in tad formation is still not fully understood. here we use our software, hicexplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) tad boundaries in drosophila melanogaster. we identify eight dna motifs enriched at boundaries, including […]

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

[…] 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 […]

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

[…] 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 […]

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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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