Last updated: 2022-02-09
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Knit directory: mage_2020_marker-gene-benchmarking/
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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]
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:
We used specific case studies to illustrate specific issues and inconsistencies with methods, especially those implemented in the scran, Scanpy and Seurat packages.
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.
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.
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.