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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

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.

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  • R 38.6%
  • Python 33.1%
  • Makefile 28.1%
  • Shell 0.2%