r3Cseq

r3Cseq is a software tool designed to simplify the interpretation of 3C-seq data. It is a R/Bioconductor package that provides a range of useful features to help researchers analyze long-range genomic interactions.

3C-seq is an innovative technique involving chromosome conformation capture (3C) coupling with next-generation sequencing technologies. This process enables the high-throughput detection of long-range genomic interactions via the generation of ligation products between DNA sequences that are closely juxtaposed in vivo. These interactions involve promoter regions, enhancers, and other regulatory and structural elements of chromosomes and can reveal key details of the regulation of gene expression.

With r3Cseq, researchers can easily perform data normalization, visualize candidate interaction regions, and detect statistically significant chromatin interactions. The tool is highly versatile and can be used in several experimental designs. This greatly facilitates hypothesis generation and the interpretation of experimental results, making it an essential tool for researchers studying long-range genomic interactions.

Topic

Sequencing

Detail

  • Operation: Sequence analysis

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.46.0

  • Credit: EU-FP7 integrated project EuTRACC, Dutch Cancer Genomics Center, the French Alternative Energies and Atomic Energy Commission, Norwegian Research Council, Bergen Research Foundation, Department of Informatics, University of Bergen.

  • Input: -

  • Output: -

  • Contact: Supat Thongjuea supat.thongjuea@ndcls.ox.ac.uk

  • Collection: -

  • Maturity: Stable

Publications

  • r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.
  • Thongjuea S, et al. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. 2013; 41:e132. doi: 10.1093/nar/gkt373
  • https://doi.org/10.1093/nar/gkt373
  • PMID: 23671339
  • PMC: PMC3711450

Download and documentation

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