Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

fourSig: a method for determining chromosomal interactions in 4C-Seq data

(2014) Rex L. Williams et al.   NUCLEIC ACIDS RESEARCH

RCircos: an R package for Circos 2D track plots

(2013) Hongen Zhang et al.   BMC BIOINFORMATICS

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

(2013) Supat Thongjuea et al.   NUCLEIC ACIDS RESEARCH

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

(2012) Erik Splinter et al.   METHODS

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

Dynamic long-range chromatin interactions controlMybproto-oncogene transcription during erythroid development

(2011) Ralph Stadhouders et al.   EMBO JOURNAL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS