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hiclib specifications


Unique identifier OMICS_12765
Name hiclib
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
mirnylib, numpy, scipy, matplotlib, h5py, cython, numexpr, statsmodels
Maintained Yes


No version available



  • person_outline Leonid A Mirny

Publication for hiclib

hiclib citations


Changes in genome organization of parasite specific gene families during the Plasmodium transmission stages

Nat Commun
PMCID: 5954139
PMID: 29765020
DOI: 10.1038/s41467-018-04295-5

[…] nning, and normalization are described in the  and source code is available from Bitbucket (https://bitbucket.org/noblelab/plasmo-hic-2018/). ICE normalization was done using iced (https://github.com/hiclib/iced). The source code for ACCOST is available at https://github.com/cookkate/ACCOST. […]


Srf destabilizes cellular identity by suppressing cell type specific gene expression programs

Nat Commun
PMCID: 5895821
PMID: 29643333
DOI: 10.1038/s41467-018-03748-1

[…] sitive -L 30 --score-min L,-0.6,-0.2 --end-to-end”; Local options: “--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end”). After read mapping, each side of the mapped reads was applied to the hiclib pipeline. First, uniquely mapped paired-reads were assigned to HindIII fragments. Only those with correct orientations were considered valid pairs, and non-ligated and self-ligated read pairs w […]


A mechanism of cohesin‐dependent loop extrusion organizes zygotic genome architecture

PMCID: 5730859
PMID: 29217590
DOI: 10.15252/embj.201798083

[…] snHi‐C data were processed similarly as in Flyamer et al (), and detailed information of single‐cell and pooled data is given in Tables and . Briefly, reads were mapped to the mm9 genome using hiclib (which applies iterative mapping with bowtie2) and then filtered. These data were then converted into Cooler files with heatmaps at different resolutions for downstream analysis.We applied the […]


Two independent modes of chromatin organization revealed by cohesin removal

PMCID: 5687303
PMID: 29094699
DOI: 10.1038/nature24281

[…] We mapped the sequence of Hi-C molecules to reference mouse genome assembly mm9 using Bowtie 2.2.8 and the iterative mapping strategy, as described in and implemented in the hiclib library for Python (publicly available at https://bitbucket.org/mirnylab/hiclib). Upon filtering PCR duplicates and reads mapped to multiple or zero locations, we aggregated the reads pairs int […]


Developmentally regulated higher order chromatin interactions orchestrate B cell fate commitment

Nucleic Acids Res
PMCID: 5737614
PMID: 28977418
DOI: 10.1093/nar/gkx722
call_split See protocol

[…] Iteratively corrected relative contact probability matrices at 40 kb resolution, generated by implementing HiResHiC module of hiclib were converted into the format specified by Domain Caller (), where the first three columns represent the chromosome number followed by start and end of the bin. Domain Caller is a simple and s […]


Activation of the alpha globin gene expression correlates with dramatic upregulation of nearby non globin genes and changes in local and large scale chromatin spatial structure

PMCID: 5504709
PMID: 28693562
DOI: 10.1186/s13072-017-0142-4

[…] Illumina HiSeq 2500 bcl2fastq v1.8.4 Conversion Software was used for base-calling. The reads were mapped independently to the region 11700000-12450000 of chromosome 14 using hiclib [] (https://bitbucket.org/mirnylab/hiclib/) iterative mapping procedure (minimal mapping length 25, iteration step 5) and Bowtie 2 version 2.2.1.Reads mapped in close proximity to DpnII restric […]


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hiclib institution(s)
Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA; Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
hiclib funding source(s)
US National Cancer Institute Physical Sciences–Oncology Center at MIT (U54CA143874); US National Institutes of Health grants HG003143 and F32GM100617; W.M. Keck Foundation Distinguished Young Scholar in Medical Research Award

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