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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