README.md

SCFormatter

SCFormatter uses singularity and snakemake workflow to handle interoperability between Seurat, SingleCellExperiment, and Scanpy anndata.

Installation

Prerequisites

• snakemake
• singularity

In ODCF clusters (e.g. worker01), singularity was installed. As for snakemake, you can use miniconda to install snakemake without root privilege.

• miniconda

Create snakemake enviroment if using conda

cd scformatter
conda env create -f snakemake.yml

Quick start

Activate snakemake enviroment

source ~/.bashrc
conda activate snakemake

Input files

Put your files under one folder with a proper filename extension. For example,

test/input/h5/
|-- GSM3489182_Donor_01_raw_gene_bc_matrices_h5.h5
`-- GSM3489185_Donor_02_raw_gene_bc_matrices_h5.h5

Filename extension (Case insensitive)

• .rds for seurat S3 object
• .h5 for 10X H5 file
• .h5ad for scanpy anndata object

Run SCBridge

python scformatter.py -h

Testing command:

python scformatter.py -t S3toH5AD -i test/input/seurat3