r3Cseq is an R package designed to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. r3Cseq was designed to perform data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.
- Linux/ Mac OsX / Windows
- R package
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Nucleic Acids Res. 2013 Jul;41(13):e132. doi: 10.1093/nar/gkt373. Epub 2013 May 13.
r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.
Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B.