CMO ACCESS Data Analysis
  • Home
  • 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
  • VAF Overview Plot Script
  • Swimmer Plot Scripts
  • Run create_report.R
  • Miscellaneous Utility Scripts
    • Convert CSV to MAF
    • Get cBioPortal Variants
    • Convert dates to days
  • Manifest Update Script
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  • 1. Installing conda
  • 2. Creating conda environment and installing R/python packages

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  1. Setup

Installation

Creating a conda environment for running the pipeline

PreviousHomeNextSetup for Running Analysis

Last updated 3 years ago

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1. Installing conda

Conda installation tutorial can be found

2. Creating conda environment and installing R/python packages

conda create --name access_data_analysis python=3
conda activate access_data_analysis
conda install r-essentials r-base r-argparse r-ggpubr r-ggthemes r-plotly r-kableextra r-htmlwidgets r-dt
pip install genotype-variants
here