Metadata-Version: 2.1
Name: methplotlib
Version: 0.2.0
Summary: Plot methylation data obtained from nanopolish
Home-page: https://github.com/wdecoster/methplotlib
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description: # METHPLOTLIB
        
        This script takes data from nanopolish as processed by calculate_methylation_frequency.py to generate a genome browser view on a window.
        
        ## INSTALLATION
        `pip install methplotlib`
        
        ## USAGE
        ```
        methplotlib [-h] -m METHYLATION [METHYLATION ...] -n NAMES [NAMES ...]
                           -w WINDOW [-g GTF] [--simplify] [--split] [--smooth SMOOTH]
        
        plotting methylation frequency
        
        optional arguments:
          -h, --help            show this help message and exit
          -m, --methylation METHYLATION [METHYLATION ...]
                                output file(s) from calculate_methylation_frequency.py
          -n, --names NAMES [NAMES ...]
                                names of datasets in --methylation
          -w, --window WINDOW   window (region) to which the visualisation has to be
                                restricted e.g. chr7:12345-23456
          -g, --gtf GTF         add annotation based on a gtf file matching to your
                                reference genome
          --simplify            simplify annotation track to show genes rather than transcripts
          --split               split, rather than overlay the methylation tracks
          --smooth SMOOTH       Smoothen the datapoints, but reduce the details (integer, default=5)
        ```
        
        
        ## TO DO - CONTRIBUTIONS WELCOME
        - Adapt to also use methylation data from tombo
        - Add plot showing (pairwise) correlation between methylation results
        - Add a mode to plot raw methylation signals rather than summarized frequencies
        - Differential methylation analysis (in windows) across groups of samples
        - Outlier detection (in windows) across samples
        - Add pipeline and visualization for phased methylation
        - Think about adding a coverage track - maybe based on the called_sites column
        
Keywords: nanopore
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Requires-Python: >=3
Description-Content-Type: text/markdown
