Last updated: 2022-04-20

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Knit directory: scFLASH/

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Metrics

Introduction.

Calculating \(p\)-values: the “implied discrete distribution.”

Fitting the droplet-based 3’ scRNA-seq dataset from Montoro et al.

  1. A preliminary look at the data.
  2. A comparison of different variance structures.
  3. An argument for backfitting.
  4. A comparison of different prior families.
  5. A discussion of size factors.
  6. A second look at pseudocounts.
  7. An attempt to use a low-rank representation of the data rather than the full data.
  8. A detailed look at a 30-factor fit.

Fitting the 3k PBMC dataset from Zheng et al.

  1. An introduction to the dataset.
  2. Variance regularization: part one.
  3. Variance regularization: part two.
  4. Prior families.
  5. Size factors.
  6. Pseudocounts.

More datasets.

  1. Deng et al.
  2. SNMF on data simulated from an NMF model: Part I. Part II.
  3. Nonnegative fits to Deng et al.
  4. Nonnegative fits to PBMCs.
  5. SNMF fit to Pijuan-Sala et al.
  6. Another Pijuan-Sala dataset.

Archived

These analyses have not necessarily been updated to use the newest version of flashier.

A brief discussion of Poisson \(p\)-values.

An early exploration of pseudocounts.

An investigation into backfitting flash-drift fits.