# TF-IDF normalization

Latent semantic indexing (LSI) was first introduced for the analysis of scATAC-seq data by [Cusanovich et al. 2018](https://www.nature.com/articles/nature25981)\[1]. LSI combines steps of frequency-inverse document frequency (TF-IDF) normalization followed by singular value decomposition (SVD). Connected Multiomics wrapped Signac's TF-IDF normalization for single cell ATAC-seq dataset. It is a two-step normalization procedure that both normalizes across cells to correct for differences in cellular sequencing depth, and across peaks to give higher values to more rare peaks\[2].

To run **TF-IDF normalization**,

* Click a **single cell ATAC counts** data node
* Click the **Normalization and scaling** section in the toolbox
* Click **TF-IDF normalization**

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 differential analysis and/or visualization.

## References

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>