Exploratory Data Analysis (EDA) Template

See the contributing guidelines for complete details and usage instructions.

Quick Start

# e.g. RNAseq, ATACseq, etc.
DATATYPE="RNAseq" 
# e.g. pAML_biomarkers, adult_AML_biomarker_validation, T-ALL_fusions, etc.
DESCRIPTION="Example_Repo" 
OUTDIR="$(date +%Y.%m.%d)_${DATATYPE}_${DESCRIPTION}"

mkdir -p $OUTDIR
cd $OUTDIR
quarto use template Meshinchi-Lab/analysis_template

Follow the prompts in the terminal to set up the template and select the default options.

You will see the following output:

Downloading [###################################] 0.0 [✓] Downloading [✓] Unzipping Preparing template files... [✓] Copying files... Files created:

• 2025-06-13_RNAseq_Example_Repo.qmd

The 2025-06-13_RNAseq_Example_Repo.qmd will be the EDA report. You can rename it if you want. You can now open the .qmd file in your favorite text editor and start editing it. When you are ready to render the HTML report, run:

quarto render 2025-06-13_RNAseq_Example_Repo.qmd