Skip to content

Ruijingfang/methylation-analysis

BranchesTags
 
 

Folders and files

NameName
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
 
 

Repository files navigation

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.

About

No description, website, or topics provided.

Resources

Readme
Activity

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

1 tags

Packages

No packages published

Languages

  • R 38.8%
  • Python 32.8%
  • Makefile 28.2%
  • Shell 0.2%