methylation-analysis

The code in this repository is the pipeline used for our nanopore methylation paper. The main script is pipeline.make which starts from data downloaded from the ENA and generates all figures and tables in the results/ directory.

Name		Name	Last commit message	Last commit date
Latest commit History 151 Commits
annotations		annotations
models		models
.gitignore		.gitignore
README.md		README.md
annotated_bed_to_tsv.py		annotated_bed_to_tsv.py
calculate_call_accuracy.py		calculate_call_accuracy.py
calculate_methylation_at_cpg_islands.py		calculate_methylation_at_cpg_islands.py
calculate_methylation_by_distance.py		calculate_methylation_by_distance.py
debug_training_plots.R		debug_training_plots.R
expand_model_alphabet.py		expand_model_alphabet.py
generate_kmer_deltas.py		generate_kmer_deltas.py
generate_training_table.py		generate_training_table.py
initialize_model.sh		initialize_model.sh
methylate_reference.py		methylate_reference.py
methylation_parsers.py		methylation_parsers.py
methylation_plots.R		methylation_plots.R
methylation_region_plot.R		methylation_region_plot.R
methylation_utils.py		methylation_utils.py
per_cg_methylation.py		per_cg_methylation.py
phase_extract.py		phase_extract.py
pipeline.make		pipeline.make
show_compute_time.py		show_compute_time.py
tsv_to_annotated_bed.py		tsv_to_annotated_bed.py

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methylation-analysis

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