Last updated: 2022-01-05

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Knit directory: single-cell-topics/analysis/

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File Version Author Date Message
Rmd 625f08a Peter Carbonetto 2022-01-05 workflowr::wflow_publish(“index.Rmd”)
Rmd 283c7ba Peter Carbonetto 2022-01-05 Working on de_analysis_mast_deseq2 R Markdown.
html f60a975 Peter Carbonetto 2022-01-05 Fixed the link.
Rmd be88eab Peter Carbonetto 2022-01-05 workflowr::wflow_publish(“index.Rmd”)
html e164b8f Peter Carbonetto 2022-01-05 Added link to overview page.
Rmd 3de0e0c Peter Carbonetto 2022-01-05 workflowr::wflow_publish(“index.Rmd”)
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Rmd 7d816c0 Peter Carbonetto 2021-12-30 workflowr::wflow_publish(“index.Rmd”, verbose = TRUE)
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Rmd b202b68 Peter Carbonetto 2021-12-30 Removed link from overview page.
html faf7ae8 Peter Carbonetto 2021-12-01 Removed a couple links from the overview page.
Rmd 4001127 Peter Carbonetto 2021-12-01 Removed the clustering and assessment of fits for the 68k pbmc data.
html 7bb3077 Peter Carbonetto 2021-11-30 Updated link on overview page.
Rmd 54d2d19 Peter Carbonetto 2021-11-30 Removed prepare_68k_pbmc analysis.
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html 5303229 Peter Carbonetto 2021-01-04 Made a few revisions to the overview page.
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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.
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Rmd 66bbdf4 Peter Carbonetto 2020-08-18 Implemented functions basic_pca_plot and pca_plot_with_labels in plots.R.
html 64b881d Peter Carbonetto 2020-08-18 Updated links in overview page.
Rmd 61917ad Peter Carbonetto 2020-08-18 Working on new analysis, plots_tracheal_epithelium.Rmd.
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Rmd 2b9f856 Peter Carbonetto 2020-08-10 wflow_publish(“index.Rmd”)
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Rmd bd72e7d Peter Carbonetto 2020-08-10 wflow_publish(“index.Rmd”)
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Rmd 67d1667 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 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