HiCPlotter 0.6.6 – Integrating HiC data with Genomic datasets

HiCPlotter 0.6.6

:: DESCRIPTION

HiCPlotter is a Python data visualization tool for integrating different data types with interaction matrixes.

::DEVELOPER

HiCPlotter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python
  • Numpy
  • Scipy
  • Cython
  • GNU Scientific Library

:: DOWNLOAD

 HiCPlotter

:: MORE INFORMATION

Citation

HiCPlotter integrates genomic data with interaction matrices.
Akdemir KC, Chin L.
Genome Biol. 2015 Sep 21;16(1):198.

HiSIF 1.0 – HiC Significant Interacting Fragments

HiSIF 1.0

:: DESCRIPTION

HiSIF is a novel computational software tool on Hi-C data analysis, including a Poisson Mixture Model, with an Expectation Maximization algorithm (EM) followed by a power-law decay background model to filter background-ligation events.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HiSIF

:: MORE INFORMATION

Citation

Zhou Y, Cheng X, Yang Y, Li T, Li J, Huang TH, Wang J, Lin S, Jin VX.
Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops.
Genome Med. 2020 Aug 12;12(1):69. doi: 10.1186/s13073-020-00769-8. PMID: 32787954; PMCID: PMC7425017.

HiCseg 1.1 – Detection of Domains in HiC data

HiCseg 1.1

:: DESCRIPTION

HiCseg allows you to detect domains in HiC data by rephrasing this problem as a two-dimensional segmentation issue.

::DEVELOPER

Céline Lévy-Leduc

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows / MacOsX
  • R

:: DOWNLOAD

 HiCseg

:: MORE INFORMATION

Citation

Two-dimensional segmentation for analyzing Hi-C data.
Lévy-Leduc C, Delattre M, Mary-Huard T, Robin S.
Bioinformatics. 2014 Sep 1;30(17):i386-i392. doi: 10.1093/bioinformatics/btu443.