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HiCPlotter specifications

Information


Unique identifier OMICS_10001
Name HiCPlotter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements
Numpy, Matplotlib, Scipy
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Lynda Chin

Publication for HiCPlotter

HiCPlotter citations

 (3)
library_books

lncRNA screen: an interactive platform for computationally screening long non coding RNAs in large genomics datasets

2017
BMC Genomics
PMCID: 5458484
PMID: 28583068
DOI: 10.1186/s12864-017-3817-0

[…] ith at least one mRNA in cis within the context of topological domains. Most importantly, mRNA expression appears to be sensitive to changes in looping with their lncRNA interacting partners. We used HiCPlotter [] to generate the Hi-C maps mRNA-lncRNA interaction plots. As an example we show the putative lncRNA CTD-2006C1.2 on chromosome 19 in Fig. . This lncRNA interacts with multiple protein-cod […]

library_books

A critical assessment of topologically associating domain prediction tools

2017
Nucleic Acids Res
PMCID: 5389712
PMID: 28334773
DOI: 10.1093/nar/gkx145

[…] d algorithm from Juicer which used as input a specialized .hic format, all other tools used different formats of binned Hi-C interaction matrices. TAD predictions from each tool were visualized using HiCPlotter (). […]

library_books

Software tools for visualizing Hi C data

2017
Genome Biol
PMCID: 5290626
PMID: 28159004
DOI: 10.1186/s13059-017-1161-y

[…] ability to process raw Hi-C reads into a contact matrix, but other toolkits are available to automate such tasks (reviewed in []). In addition to the tools we reviewed here, software packages such as HiCplotter [] and HiTC [] offer visualization capabilities but require programming capabilities.We have discussed visualization of raw or normalized Hi-C data, but other transformations of the data ca […]


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HiCPlotter institution(s)
Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

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