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TF-IDF normalization in Flow can be invoked in Normalization and scaling section by clicking any single cell counts data node (Figure 1).

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Figure 1. TF-IDF normalization task in Normalization and scaling section in Flow.

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The output of TF-IDF normalization is a new data node that has been normalized by log(TF x IDF). We can then use this new normalized matrix for downstream analysis and visualization (Figure 2).

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Figure 2. Example workflows to demonstrate downstream analysis and visualization of TF-IDF normalization output.

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1. 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
2. https://satijalab.org/signac/index.html

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