Last updated: 2021-11-30

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Knit directory: single-cell-topics/analysis/

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Rmd 54d2d19 Peter Carbonetto 2021-11-30 Removed prepare_68k_pbmc analysis.
html 2befadb Peter Carbonetto 2021-11-08 Added link to overview page.
Rmd 71e267d Peter Carbonetto 2021-11-08 workflowr::wflow_publish(“index.Rmd”)
html f2cd3c7 Peter Carbonetto 2021-10-20 Fixed link in overview page.
Rmd 27b2d08 Peter Carbonetto 2021-10-20 workflowr::wflow_publish(“index.Rmd”)
html ed35cd9 Peter Carbonetto 2021-10-18 Added link to overview page.
Rmd 681296e Peter Carbonetto 2021-10-18 workflowr::wflow_publish(“index.Rmd”)
html da1a3c6 Peter Carbonetto 2021-10-09 Added link to home page.
Rmd 3be2035 Peter Carbonetto 2021-10-09 workflowr::wflow_publish(“index.Rmd”)
Rmd 4e298d9 Peter Carbonetto 2021-01-06 Small edit to overview page.
html 5303229 Peter Carbonetto 2021-01-04 Made a few revisions to the overview page.
Rmd b6f77c1 Peter Carbonetto 2021-01-04 workflowr::wflow_publish(“index.Rmd”)
Rmd 5b1983f Peter Carbonetto 2021-01-03 A few minor changes to the analysis of the purified PBMC data.
html 134ea78 Peter Carbonetto 2021-01-03 Updated the overview page.
Rmd 83151f0 Peter Carbonetto 2021-01-03 workflowr::wflow_publish(“index.Rmd”)
Rmd 56b9684 Peter Carbonetto 2020-12-29 Added new section to overview page on single-cell likelihoods.
Rmd 0ef8a20 Peter Carbonetto 2020-11-26 Working on solving purified PBMC ‘mysteries’.
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Rmd be55916 Peter Carbonetto 2020-07-26 wflow_publish(“index.Rmd”)
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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 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