Latent semantic indexing (LSI)  was first introduced for the analysis of scATAC-seq data by Cusanovich et al. 2018[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].

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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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