Preprocessing: PP#
Data integration#
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Batch balanced kNN [Polanski19]. |
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Use harmonypy [Korunsky19] to integrate different experiments. |
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Correct batch effects by matching mutual nearest neighbors [Haghverdi18] [Kang18]. |
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Use Scanorama [Hie19] to integrate different experiments. |
Sample demultiplexing#
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Probabilistic demultiplexing of cell hashing data using HashSolo [Bernstein20]. |
Imputation#
Note that the fundamental limitations of imputation are still under debate.
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Deep count autoencoder [Eraslan18]. |
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Markov Affinity-based Graph Imputation of Cells (MAGIC) API [vanDijk18]. |