Code from the chromatin variation 3d project
By Oana Ursu
Contact: oursu@stanford.edu
Contents
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browserTracks - code for creating the browser tracks displayed at http://chromovar3d.stanford.edu
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DNase - code for processing the DNase data
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GWASnetworks - code for the GWAS network analysis
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MotifAnalysis - code for computing correlation between signal and TF motif scores across individuals
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RNAseq - code for processing the RNAseq data
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SNPs - code for merging together the SNP set used in this analysis
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peakCalling - code for processing the histone mark data for H3K4me1, H3K4me3, H3K27ac
More code from this paper
For code related to the QTL calling, and HiC quantification and enrichment refer to Judith Zaugg's page at http://www.zaugg.embl.de/data-and-tools/distal-chromatin-qtls/