timoast / epi-immune

Processing pipeline for public multiome and scATAC-seq immune datasets

Immune cell public epigenomic data

Processing pipeline for public single-cell epigenomic immune datasets.

Installing dependencies

All the required dependencies needed to run the workflow can be installed automatically by creating a new conda environment.

First ensure that conda or mamba is installed and available.

To create a new environment with the dependencies installed, run:

# using conda
conda env create -f environment.yaml

# using mamba
mamba env create -f environment.yaml

Running the workflow

This workflow involves downloading data from AWS using the AWS command line tools. To enable the download, you will first need to create an AWS account and set up the AWS command line tools by running aws configure. Note that some of the data downloaded may incur charges from AWS.

To run the Snakemake workflow, first activate the conda environment containing the required dependencies:

conda activate immune

Next, run snakemake with the desired options. Setting the -j parameter controls the maximum number of cores used by the workflow:

snakemake -j 24

See the snakemake documentation for a complete list of available options.

Datasets

PBMC

pbmc_atac_500

pbmc_atac_1k

pbmc_atac_5k

pbmc_atac_10k

pbmc_atac_10k_chromium

pbmc_atac_10k_chromiumX

pbmc_multiome_3k_sorted

pbmc_multiome_3k_unsorted

pbmc_multiome_10k_sorted

pbmc_multiome_10k_unsorted

pbmc_multiome_10k_chromium

pbmc_multiome_10k_chromiumX

pbmc_reference

BMMC

bmmc_atac

bmmc_multiome

bmmc_reference