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Once we have filtered a list of significantly different differentially expressed genes, we can visualize these genes by generating a heatmap(Link), performing Geneset , or perform the Gene set enrichment analysis and motif detection. 

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For information about automating steps in this analysis workflow, please see our documentation page on Making a Pipeline. 

References

Soneson C and Robinson MD. Bias, robustness and scalability in single-cell differential expression analysis. Nature Methods 2018 Apr;15(4):255-261. 

1. https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
2. Cusanovich, D., Reddington, J., Garfield, D. et al. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature 555, 538–542 (2018). https://doi.org/10.1038/nature25981
3. https://satijalab.org/signac/index.html
4. https://support.10xgenomics.com/single-cell-atac/software/visualization/latest/tutorial-celltypes

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