The coupling of chromosome conformation capture (3C) with next-generation 
sequencing technologies enables the high-throughput detection of long-range 
genomic interactions, via the generation of ligation products between DNA 
sequences, which 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. 
3C-seq is a variant of the method for the detection of interactions between one 
chosen genomic element (viewpoint) and the rest of the genome. We present 
r3Cseq, an R/Bioconductor package designed to perform 3C-seq data analysis in a 
number of different experimental designs. The package reads a common aligned 
read input format, provides data normalization, allows the visualization of 
candidate interaction regions and detects statistically significant chromatin 
interactions, thus greatly facilitating hypothesis generation and the 
interpretation of experimental results. We further demonstrate its use on a 
series of real-world applications.