├── .gitignore ├── Figure_S2.pdf ├── LICENSE ├── README.md ├── Snakefile ├── bioc_requirements.txt ├── dependency_graph.svg ├── environment.yml ├── genome_data ├── CGI_coordinates_mm10.masked.HMM.tsv ├── ICR_plot_regions.tsv ├── known_imprinted_genes.RData └── primary_ICRs_mm10.tsv ├── haplotype_dependency_graph.svg ├── install_R_deps.R ├── make_graphs.sh ├── md5 ├── bisulfite │ ├── B6CastF1_1_R1.fastq.gz.md5 │ ├── B6CastF1_1_R2.fastq.gz.md5 │ ├── B6CastF1_2_R1.fastq.gz.md5 │ ├── B6CastF1_2_R2.fastq.gz.md5 │ ├── B6CastF1_5_R1.fastq.gz.md5 │ ├── B6CastF1_5_R2.fastq.gz.md5 │ ├── B6CastF1_6_R1.fastq.gz.md5 │ └── B6CastF1_6_R2.fastq.gz.md5 ├── nanopore │ ├── 2017_05_03.b6xcast.minion.fast5.tar.gz.md5 │ ├── 2017_05_12.b6xcast.minion.fast5.tar.gz.md5 │ ├── 2017_05_25.b6xcast.minion.fast5.tar.gz.md5 │ ├── b6.minion.fast5.tar.gz.md5 │ ├── b6.minion.methylation.tsv.gz.md5 │ ├── b6xcast.minion.methylation.tsv.gz.md5 │ ├── cast.minion.fast5.tar.gz.md5 │ ├── cast.minion.methylation.tsv.gz.md5 │ ├── castxb6.promethion.fast5.tar.gz.md5 │ └── castxb6.promethion.methylation.tsv.gz.md5 └── rna_seq │ ├── B6CastF1_2_R1.fastq.gz.md5 │ ├── B6CastF1_2_R2.fastq.gz.md5 │ ├── B6CastF1_3_R1.fastq.gz.md5 │ ├── B6CastF1_3_R2.fastq.gz.md5 │ ├── B6CastF1_4_R1.fastq.gz.md5 │ ├── B6CastF1_4_R2.fastq.gz.md5 │ ├── B6CastF1_5_R1.fastq.gz.md5 │ ├── B6CastF1_5_R2.fastq.gz.md5 │ ├── CastB6F1_2_R1.fastq.gz.md5 │ ├── CastB6F1_2_R2.fastq.gz.md5 │ ├── CastB6F1_3_R1.fastq.gz.md5 │ ├── CastB6F1_3_R2.fastq.gz.md5 │ ├── CastB6F1_4_R1.fastq.gz.md5 │ ├── CastB6F1_4_R2.fastq.gz.md5 │ ├── CastB6F1_5_R1.fastq.gz.md5 │ └── CastB6F1_5_R2.fastq.gz.md5 ├── methylation_dependency_graph.svg ├── notebooks ├── b6_haplotype_analysis.Rmd ├── b6xcast_haplotype_analysis.Rmd ├── cast_haplotype_analysis.Rmd ├── castxb6_haplotype_analysis.Rmd ├── compare_detected_dmrs.Rmd ├── differential_methylation_heatmaps.Rmd ├── genome_level_methylation_summary.Rmd ├── nanopolish_fvb_resolution.Rmd ├── nanopolish_methylation_validation.Rmd ├── rnaseq_analysis.Rmd ├── single_strain_auc.Rmd ├── snp_quality_score_analysis.Rmd └── visualise_dmr.Rmd ├── r_requirements.txt ├── requirements.txt ├── rnaseq_dependency_graph.svg └── scripts ├── allelic_methylation.snakefile ├── build_dss_dmrlist.R ├── build_methylation_df.R ├── build_supplementary_db.py ├── calculate_methylation_frequency.py ├── call_variant_proportion.py ├── compare_haplotype_methylation.py ├── count_cpg.py ├── dss_paired.R ├── ensembl_gtf_to_tsv.R ├── environment.yml ├── fit_reads.R ├── fvb_resolution.snakefile ├── intermediate.snakefile ├── mask_genome_variants.py ├── merge_recombined_haplotypes.py ├── misc.snakefile ├── nanopolish.snakefile ├── notebooks.snakefile ├── prepare_visualisation.R ├── read_haplotypes.R ├── read_summary.R ├── render_notebook.R ├── rna_seq.snakefile ├── rrbs.snakefile ├── split_methylation_by_alignment.py ├── split_methylation_by_haplotype.py ├── summarize_bisulfite_methylation.py └── tsv_to_region.py /.gitignore: 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