Last updated: 2022-02-09

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Knit directory: mage_2020_marker-gene-benchmarking/

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Project overview

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

Our findings are summarized in the manuscript:

[TODO]

Analyses

Method comparison

We assessed the method’s

We compared the methods using both simulated and real datasets across a range of criteria.

TODO: Fit in:

Methods were also compared on their ability to select expert derived marker genes in different datasets:

Datasets

A variety of scRNA-seq datasets are used in the used to compare methods. For theses datasets we have performed general analysis, including selecting marker genes. The code used to process the each dataset can be found in the corresponding prep_* R script in the code directory.

Other analyses

Finally, other analyses included in this repository were used in the MSc thesis this project was originally conceived as. They may, however, be of independent interest.


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