Last updated: 2022-01-05

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Knit directory: single-cell-topics/analysis/

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Evaluation of DE analysis using a topic model

In these pages, we assess the new topic-model-based methods for differential expression analysis, and compare with MAST and DESeq2.

Data preparation

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

Assess Poisson NMF 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 identify clusters of cells from the mixture proportions.

Visualize and annotate topics

In these pages, we annotate topics and substructures to determine their biological relevance. This includes differential expression analysis using the topic model.

Examine single-cell likelihoods

In these pages, we calculate single-cell likelihoods to assess how well the multinomial topic model captures expression in different cells and cell types.

Other analyses