/n1diff

Differential gene expression with James-Stein estimators

Primary LanguageHTMLMIT LicenseMIT

Hedging uncertainty in differential gene expression analyses with James-Stein estimators

Code, data, and analysis for a chapter of my PhD thesis. The code for calculating the James-Stein fold change estimates can be found in code/jse-shrinkage/jse.R.

Usage

This repository is structured as follows:

.
├── data/            # directory where all non-analysis data is stored
└── code/
    ├── result1/     # analysis scripts for `result1`
    ├── result2/     # analysis scripts for `result2`
    └── ...
└── results/
    ├── result1/     # results and plots, generated from `/code/result1/`
    ├── result2/     # results and plots, generated from `/code/result2/`
    └── ...
├── README.md        # this file
└── environment.yaml # Anaconda environment YAML file for the entire project

To re-run any of the analyses in the code/ folders:

  1. Build and activate the conda environment stored in environment.yaml 
    conda create --file environment.yaml -n <ENV_NAME>
conda activate <ENV_NAME>
  2. Navigate to the result directory of interest
  3. Run snakemake

That will regenerate the entire set of results for that specific folder. You can preview that needs to be run by running snakemake -n before running the analyses.