scHiCNorm – Eliminate Systematic Biases in Single-cell Hi-C data

scHiCNorm

:: DESCRIPTION

scHiCNorm is a software package for eliminating systematic biases in single-cell Hi-C data. Considering that single-cell Hi-C data are zero-inflated, here we use zero-inflated (Poisson and Negative Binomial) and hurdle (Poisson and Negative Binomial) models to remove biases, including cutting sites, GC content, and mappability.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

scHiCNorm

:: MORE INFORMATION

Citation

Liu T, Wang Z.
scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data.
Bioinformatics. 2018 Mar 15;34(6):1046-1047. doi: 10.1093/bioinformatics/btx747. PMID: 29186290; PMCID: PMC5860379.

TADtree – Identification of Hierarchical Topological Domains in Hi-C data

TADtree

:: DESCRIPTION

TADtree is an algorithm the identification of hierarchical topological domains in Hi-C data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
Python

:: DOWNLOAD

TADtree

:: MORE INFORMATION

Citation:

Identification of hierarchical chromatin domains.
Weinreb C, Raphael BJ.
Bioinformatics. 2015 Aug 26. pii: btv485

MetaPhase – Metagenomic Deconvolution with Hi-C

MetaPhase

:: DESCRIPTION

MetaPhase is a software tool to perform metagenomic deconvolution. That is, it inputs a metagenome assembly – an assembly created from a mixed genomic sample, usually of many different microbial species – and it determines which contigs in that assembly belong together in the same genomes. A metagenome assembly does not contain the complete genomes of any one species in the mixed sample, but the deconvoluted assembly can contain nearly complete genomes of many individual species. MetaPhase relies on data generated by Hi-C, an established molecular technique of studying chromatin conformation.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++

:: DOWNLOAD

MetaPhase

:: MORE INFORMATION

Citation

Burton JN, Liachko I, Dunham MJ, Shendure J.
Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps.
G3 (Bethesda). 2014 May 22;4(7):1339-46. doi: 10.1534/g3.114.011825. PMID: 24855317; PMCID: PMC4455782.

tREX – Reconstruction of 3D structure of Chromatins using Hi-C data

tREX

:: DESCRIPTION

tPAM and tREX(truncated Random effect EXpression) are codes for reconstruction of 3D structure of chromatins using Hi-C data based on two model-based algorithms.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

tREX

:: MORE INFORMATION

Citation

BMC Bioinformatics, 17, 70 2016 Feb 6
Impact of Data Resolution on Three-Dimensional Structure Inference Methods
Jincheol Park, Shili Lin

ChromSDE 2.2 – Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data

ChromSDE 2.2

:: DESCRIPTION

ChromSDE is a deterministic method , which applies semi-definite programming techniques to find the best structure fitting the observed data and uses golden section search to find the correct parameter for converting the contact frequency to spatial distance.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
MatLab

:: DOWNLOAD

ChromSDE

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Nov;20(11):831-46. doi: 10.1089/cmb.2013.0076.
3D chromosome modeling with semi-definite programming and Hi-C data.
Zhang Z, Li G, Toh KC, Sung WK.

CytoHiC 1.1 – Visual Comparison of Hi-C Networks

CytoHiC 1.1

:: DESCRIPTION

CytoHiC is a plugin for the Cytoscape platform which allows users to view and visually compare spatial maps of genomic landmarks, based on normalized Hi-C data.

::DEVELOPER

CytoHiC team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java
Cytoscape

:: DOWNLOAD

CytoHiC

:: MORE INFORMATION

Citation

CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks.
Yoli Shavit; Pietro Lio’.
Bioinformatics 2013; doi: 10.1093/bioinformatics/btt120