title: r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.
abstract: 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.
authors.affiliation: Computational Biology Unit, Uni Computing, Uni Research AS, N-5020 Bergen, Norway.
authors.forename: Supat
authors.initials: S
authors.lastname: Thongjuea
authors.forename: Ralph
authors.initials: R
authors.lastname: Stadhouders
authors.forename: Frank G
authors.initials: FG
authors.lastname: Grosveld
authors.forename: Eric
authors.initials: E
authors.lastname: Soler
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D002875:Chromosomes / Q000737:chemistry*; D020570:Genes, myb; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D017422:Sequence Analysis, DNA; D012984:Software; D055544:beta-Globins / Q000235:genetics
chemical_list: D055544:beta-Globins