This workbook contains code to reproduce the figures of the paper GARDEN-NET and ChAseR: a suite of tools for the analysis of chromatin networks showing examples of the usage of the ChAseR package on Promoter Capture HiC data for haematopoietic cells (Javierre et al. Cell 2016) in integration with gene expression, methylation and histone modification data in the same cell types (neutrophils,monocytes and Tcells Chen et al. Cell 2016) and replication timing.
Data sources Data for the Chen et al. Cell 2016 can be found here ftp://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/ (histone modifications extracted from the /data directory, expression and methylation from the /Pheno_Matrix folder. The Promoter Capture HiC data from Javierre et al. Cell 2016 can be downloaded from https://osf.io/u8tzp/, we used cutoff 5, as suggested by CHiCAGO guidelines (Cairns et al. Genome Biology 2016)