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chromosome conformation capture analysis bioinformatics software tools

The 3C method uses formaldehyde cross-linking to covalently link interacting chromatin segments in intact cells. Cross-linked chromatin is then solubilized and digested with an appropriate restriction enzyme. This is followed by intramolecular…
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r3Cseq
Desktop

r3Cseq

An R/Bioconductor package for the discovery of long-range genomic interactions…

An R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.

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InfMod3DGen
Desktop

InfMod3DGen

A Bayesian framework to derive the 3D architecture of a chromosome from…

A Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. InfMod3DGen can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance…

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chromoHBM/chrom…
Desktop

chromoHBM/chromoHBM-3D/chromoHBM-3C

An algorithmic framework, which is based on hierarchical block matrices (HBMs),…

An algorithmic framework, which is based on hierarchical block matrices (HBMs), for topological analysis and integration of chromosome conformation capture (3C) data. We first describe chromoHBM, an…

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Lollipop
Desktop

Lollipop

Assists in making genome-wide predictions of CCCTC-binding factor…

Assists in making genome-wide predictions of CCCTC-binding factor (CTCF)-mediated loops. Lollipop is a machine-learning framework based on random forests classifier. It accounts for the complexity of…

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Multicontactchr…
Dataset

Multicontactchromatin

Allows for high resolution analysis of spatial DNA sequence co-occurrence…

Allows for high resolution analysis of spatial DNA sequence co-occurrence frequencies at the single allele level. Multicontactchromatin is an online resource that assists users in the calculation of…

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