SIMBA is a method to embed cells along with their defining features such as gene expression, transcription factor binding sequences and chromatin accessibility peaks into the same latent space.
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Preprint: Huidong Chen, Jayoung Ryu, Michael E. Vinyard, Adam Lerer & Luca Pinello.
“SIMBA: SIngle-cell eMBedding Along with features. bioRxiv, 2021.10.17.464750v1 (2021).”