Repository to perform RNAseq analysis in sea urchin embryos between ethanol treated and control embryos.

Installation

To install the pipeline, you will need to have the following tools installed in your environemnt:

1. Snakemake
2. Python 3
3. Python libraries pandas and numpy
4. R
5. R packages sva, gsva, deseq2, and ggplot2

Data availability

The data is available on GEO at GSE207100

Running the pipeline:

To run the pipeline, adust the necessary file paths in config.yaml to match your file system, then simply navigate to this repository and issue the command:

snakemake -j<number_of_jobs_to_run>