HiCdat: a fast and easy-to-use Hi-C data analysis tool

[11] Selvaraj S(2011)Two-dimensional segmentation for analyzing Hi-C data Nat Genet 43 1059-65

[12] Yue F(2012)Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data Bioinformatics 28 3131-3

[13] Kim A(2010)Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture Mol Cell 38 576-89

[14] Li Y(2012)HiCNorm: removing biases in Hi-C data via Poisson regression Nat Methods 9 999-1003

[15] Shen Y(2014)Simple combinations of lineage-determining transcription factors prime Bioinformatics 30 1620-22

[16] Moissiard G(2013)-regulatory elements required for macrophage and B cell identities Nucleic Acids Res 41 108-4

[17] Cokus SJ(2013)Iterative correction of Hi-C data reveals hallmarks of chromosome organization Nature 503 290-93

[18] Cary J(2009)HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization Science 326 289-21

[19] Feng S(2012)The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote Cell 148 908-9

[20] Billi AC(2013)A high-resolution map of the three-dimensional chromatin interactome in human cells Genome Biol 14 129-66

[11] Selvaraj S(2011)Two-dimensional segmentation for analyzing Hi-C data Nat Genet 43 1059-65

[12] Yue F(2012)Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data Bioinformatics 28 3131-3

[13] Kim A(2010)Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture Mol Cell 38 576-89

[14] Li Y(2012)HiCNorm: removing biases in Hi-C data via Poisson regression Nat Methods 9 999-1003

[15] Shen Y(2014)Simple combinations of lineage-determining transcription factors prime Bioinformatics 30 1620-22

[16] Moissiard G(2013)-regulatory elements required for macrophage and B cell identities Nucleic Acids Res 41 108-4

[17] Cokus SJ(2013)Iterative correction of Hi-C data reveals hallmarks of chromosome organization Nature 503 290-93

[18] Cary J(2009)HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization Science 326 289-21

[19] Feng S(2012)The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote Cell 148 908-9

[20] Billi AC(2013)A high-resolution map of the three-dimensional chromatin interactome in human cells Genome Biol 14 129-66