# 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). Partek Flow 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]. **TF-IDF normalization** in Flow can be invoked in *Normalization and scaling* section by clicking any single cell counts data node (Figure 1).
Figure 1. TF-IDF normalization task in Normalization and scaling section in Flow.
To run **TF-IDF normalization**, * Click a **single cell 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 analysis and visualization (Figure 2).
Figure 2. Example workflows to demonstrate downstream analysis and visualization of TF-IDF normalization output.
## 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). 2. ## Additional Assistance If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.