Last updated: 2021-04-13

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Knit directory: mage_2020_marker-gene-benchmarking/

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Rmd 581627b Jeffrey Pullin 2021-04-13 Rebuild index
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Rmd 63bce66 Jeffrey Pullin 2021-02-16 Add new marker gene type analysis and update FDR + TPR
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Rmd 7971ea2 Jeffrey Pullin 2020-10-25 Initial commit

Project overview

This project aim to benchmark current methods for the detection of cell-type maker genes in scRNA-seq data

Analyses

Simulation analyses

The methods were compared on several criteria:

  1. Speed

  2. TPR

  3. FDR control

  4. FDR curves

  5. ROC curves

  6. Concordance of results

Simulation

The simulations estimate parameters from the following data sets:

  1. Lawlor

The simulations are visualized in:

  1. Simulation visualistions

Datasets and simulations are compared using countsimQC

  1. CountsimQC