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Code used to create figures in the 2016 paper A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets.

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Figure_1_Unsupervised_hierarchical_clustering_of_DNA_methylation.R
Figure_1_Unsupervised_hierarchical_clustering_of_DNA_methylation.R
 
 
Figure_2_Identification_of_subsets_if_loci_with_distinctive_progressive_changes_in_DNA_methylation.R
Figure_2_Identification_of_subsets_if_loci_with_distinctive_progressive_changes_in_DNA_methylation.R
 
 
Figure_3_The_genomic_contexts_of_loci_gaining_or_losing_DNA_methylation.R
Figure_3_The_genomic_contexts_of_loci_gaining_or_losing_DNA_methylation.R
 
 
Figure_4_Overlap_of_loci_with_distinctive_DNA_methylation_with_sites_of_transcription_factor_binding_in_HepG2_cells.R
Figure_4_Overlap_of_loci_with_distinctive_DNA_methylation_with_sites_of_transcription_factor_binding_in_HepG2_cells.R
 
 
Figure_5_Analysis_of_gene_expression_data_from_the_samples_tested_for_DNA_methylation_changes.R
Figure_5_Analysis_of_gene_expression_data_from_the_samples_tested_for_DNA_methylation_changes.R
 
 
Figure_6_Functional_properties_of_genes_targeted_for_DNA_methylation_and_transcriptional_changes.R
Figure_6_Functional_properties_of_genes_targeted_for_DNA_methylation_and_transcriptional_changes.R
 
 
Figure_S3_S6_prin_components.R
Figure_S3_S6_prin_components.R
 
 
Figure_S4_Expression_TFsl.R
Figure_S4_Expression_TFsl.R
 
 
Figure_S5_Bcell.R
Figure_S5_Bcell.R
 
 
Figure_S8_CGl.R
Figure_S8_CGl.R
 
 
README.md
README.md
 
 
bedTools.2in.R
bedTools.2in.R
 
 
bed_boot.R
bed_boot.R
 
 

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HCV_Wijetunga_et_al_2016

Code used to create figures in the 2016 paper A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets.

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Code used to create figures in the 2016 paper A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets.

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