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CMO ACCESS Data Analysis
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Github codebase
Setup
Installation
Setup for Running Analysis
Resources
CNA Result Processing
Analysis
Overview of Analysis Workflow
Compile Reads
Filter Calls
SV Incorporation
CNA Processing
Create Patient Report
Intermediate File Organization
Miscellaneous Utility Scripts
Convert CSV to MAF
Get cBioPortal Variants
Convert dates to days
Run create_report.R
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ACCESS Data Analysis
Scripts for downstream analysis plotting of ACCESS variant calling pipeline output
This gitbook will walk you through:
  • ​Setup​
    • ​Installation​
    • ​Master file creation​
    • ​Resource files​
  • ​Analysis​
    • ​Overview of Analysis Workflow​
    • ​Compile Reads​
    • ​Filter Calls​
    • ​SV Incorporation​
    • ​CNA Processing​
    • ​Create Patient Report​
    • ​Intermediate file structure​
  • ​Miscellaneous Utility Scripts​
    • ​Convert CSV to MAF​
    • ​Get cbioportal variants​
    • ​Convert dates to days​
    • ​Run create_report.R​
​
Next - Setup
Installation
Last modified 2mo ago
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