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INCLUDE TR01 PROJECT

Dependencies

  • miniforge - check out miniforge. This repository holds the minimal installers for Conda and Mamba specific to conda-forge. Distribution >= Miniforge3-22.3.1-0.

  • snakemake and other requirements

mamba env create -f environment.yml

Run analyses

Activate the conda environment

mamba activate snakemake

Workflow can be executed by:

-j defines the number of cores or jobs to be used in parallel processing. For example, make -j 1 would use 1 core.

snakemake --use-conda --snakefile include_tr01.smk -j 1

Datasets

GTEx

Within this repository, we obtain the GTEx Analysis V8 Gene TPMs data through the GTEx Portal, further process it, and apply PLIER.