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# Snakemake Workflow: single cell RNA-seq analysis
The chosen methods are based on the paper of Luecken and Theis, 2019 (https://doi.org/10.15252/msb.20188746), explaining the current best practice in single cell RNA-seq analysis.
The chosen methods are based on the paper of Luecken and Theis, 2019 (https://doi.org/10.15252/msb.20188746), explaining the current best practice in single cell RNA-seq analysis, and has been extended to multimodal analysis using Specter (https://www.biorxiv.org/content/10.1101/2020.06.15.151910v1). We are currently preparing a standalone application of Specter that will no longer require a MATLAB license by the user.
## Installations
* install Snakemake (workflow management system)
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