Seismic Graph Documentation

seismic-graph is a python package that generates plots and analysis from mutational profile data. seismic-graph is built to work with DMS-MaPseq data processed by SEISMIC-RNA. seismic-graph also has a built in converter that can read mutational data processed by ShapeMapper2 or RNA Framework.

We recognize that many users may not have the requisite python skills to use a python package, and for them we have built SEISMICgraph, a webapp that allows users to take advantage of the features of seismic-graph without writing any code.

This documentation covers both seismic-graph the python package, and SEISMICgraph the webapp.

Table of Contents

• SEISMICgraph: Web App Documentation
  • Overview
  • Workflow for SEISMICgraph
  • SEISMICgraph: Step by Step walkthrough
• seismic-graph: Python Package Documentation
  • Install seismic-graph
  • Import your data into a study object
  • Make a plot
  • Outlier filtering
  • Normalize
• Gallery
  • Base coverage
  • Compare mutation profiles
  • Correlation by refs between samples
  • Experimental variable across samples
  • Mutation fraction
  • Mutation fraction delta
  • Mutation fraction identity
  • Mutation per read per reference
  • Mutations per read per sample
  • Num aligned reads per reference frequency distribution
• Compatible Data Formats
  • Overview
  • SEISMIC-RNA webapp json
  • RNAFramework
  • ShapeMapper2