MUFFIN : A suite of tools for the analysis of functional sequencing data - Code

View on Github : https://github.com/pdelangen/Muffin 

Installation

Muffin can be installed through conda. Right now it is only available on a private channel, but it is planned to migrate to conda-forge or bioconda. We highly recommend starting from a fresh environment (and optionally to use mamba instead of conda, which resolves conflicts faster and better than conda):

# Change ENV_NAME to the name of your choice, and add OTHER_PACKAGES if needed
conda install -c conda-forge mamba
mamba create -n ENV_NAME -c pdelangen13 -c bioconda -c conda-forge muffin OTHER_PACKAGES
conda activate ENV_NAME

To use the dependencies versions used at build time, you can use the provided yml file :

conda install -c conda-forge mamba
mamba env create -f environment_muffin.yml

Guidelines, examples and API reference are available on ReadTheDocs.

Clone the repository :

git clone https://github.com/pdelangen/Muffin

Download the data from Zenodo (~3GB compressed).

And use the notebooks located in docs/examples.

If you really wish to reproduce the H3K4Me3 ChIP-seq analysis (WARNING : it will download around 100GB of data from ENCODE), you will need to run the the snakemake script "dl_data.smk" located in the immune_chip/ folder downloaded from the zenodo repository.

If you use Muffin in your work, please cite :

MUFFIN : A suite of tools for the analysis of functional sequencing data
Pierre de Langen, Benoit Ballester
bioRxiv 2023.12.11.570597; doi: https://doi.org/10.1101/2023.12.11.570597