Metadata-Version: 2.1
Name: mafViper
Version: 0.1
Summary: A Python package for processing, analyzing and visualizing MAF files.
Home-page: https://github.com/jrosen-code/mafViper
Author: Joseph Rosen
Author-email: joemrosen@gmail.com
License: UNKNOWN
Description: # mafViper Documentation
        
        A python package for reading, analyzing and visualizing mutation annotation files
        
        ## Features
        
        - Load and validate MAF files as pandas DataFrames.
        
        - MAF processsing and classification tools (i.e synonymous vs. non-synonymous)
        
        - Merge multiple MAF files into a single DF. 
        
        - Generate mutation summary plots, and Ti/Tv analyses. 
        
        
        ## Current Functions
        
        * **read_maf**: 
        	- Loads a maf file into the env as a pandas df and validates columns
        	- allows for somatic vs. non-somatic selection with useAll parameter
        
        * **classify_variants**:
        	- Seperates variants into synonymous and non-synonmous categories
        	- discard_synonymous (default True) allows you to drop synonymous mutations from dataframe
        * **merge_mafs**:
        	- merges a list of maf files into one maf
        	- discard_synonymous parameter allows you to drop synonymous mutations after merge
        * **get_titv**:
        	- Classifies SNVs into Ti/Tv and returns a summary df for plotting and analyses
        	- Summary df contains SNV class, Raw counts by class, and fractional proportions of each class 
        
        * **get_maf_summary**:
        	- creates a set of maf summary analysis plots and pdf per user input 
        	- Top Mutated Genes plot (default 10)
        	- Stacked Bar chart for Variants Per Sample (add stat line- default median)
        	- Variant Classifaction Summary Plot
        	- Boxplot of variant classes 
        	- SNV Class summary  plot(Ti/Tv data visualization)
        	- Variant Type summary plot (SNP, INS, DEL, etc)
        
        ## Installation
        
        '''bash
        
        pip install mafViper
        
         
        
Platform: UNKNOWN
Requires-Python: >=3.9
Description-Content-Type: text/markdown
