Last updated: 2020-11-13

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Knit directory: single-cell-topics/analysis/

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Data preparation

These pages detail the steps taken to prepare the single-cell RNA-seq data sets for topic modeling analysis.

Assess model fits

In these pages, we compare the quality of the Poisson NMF fits with different updates (EM, CCD, SCD, with and without extrapolation), and with different settings for \(K\).

Identify clusters

In these pages, we perform PCA on the estimated topic proportions, and use this to identify clusters.

Perform differential expression analysis

In these pages, we perform a differential expression analysis using a topic model and clusters identified from this topic model.

Visualize and interpret topics

TO DO: Add brief description here.