Open aopisco opened 3 years ago
I like the idea of this and think benchmarking marker gene identification would be very impactful... but how do you define ground truth marker genes? Are these genes derived from the literature (usually surface markers)? Or are these markers that are validated across batches and datasets (sounds like a very tough task)?
We have a compiled list of marker genes from the literature and expert groups that are mostly but not exclusively surface markers. We could start there?
I think that sounds fair. Ideally this task would have a second dataset with marker genes that are not mostly surface markers to show some diversity of test cases. Could we come up with a second dataset as well?
Describe the problem concisely. Cell types are historically characterized by morphology and functional assays, but one of the main advantages of single-cell transcriptomics is their ability to define cell identities and their underlying regulatory networks. We have developed scRFE to produce interpretable gene lists for all cell types in a given dataset that can be used to design experiments or to further aid with biological data mining, but it would be great to benchmark scRFE and other methods in the community
Propose datasets So far we used Tabula Muris Senis
Propose methods NEED TO DO
Propose metrics Compare with ground truth marker genes (https://docs.google.com/spreadsheets/d/1SsKS2vMvZqLdJ8hOv_dBeXo3k4Gcwcy-oPBhFTCo0tY/edit?usp=sharing)