Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Citations
7,892 citations
Cites background or methods or result from "Integrating single-cell transcripto..."
...To overcome this, we first jointly reduce the dimensionality of both datasets using diagonalized CCA, then apply L2-normalization to the canonical correlation vectors (Figures 1A and 1B)....
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...We also tested the following existing integration methods on the same holdout datasets: Seurat v2 [Butler et al., 2018], mnnCorrect [Haghverdi et al., 2018], and scanorama [Hie et al., 2019]....
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...Canonical correlation vectors are calculated as described previously [Butler et al., 2018]....
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...3.3 Butler et al., 2018 https://github.com/satijalab/seurat/releases/tag/ v2....
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...For Seurat v2, we used the same feature set as determined for Seurat v3 to run a multi-CCA analysis followed by alignment (RunMultiCCA and AlignSubspace in Seurat v2)....
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3,016 citations
2,924 citations
Cites result from "Integrating single-cell transcripto..."
...We note that in contrast to our previously developed scRNA-seq integration algorithms [37, 54], the reference dataset and visualization can remain constant during this procedure....
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2,459 citations
2,037 citations
Cites methods or result from "Integrating single-cell transcripto..."
...As we have previously demonstrated [Butler et al., 2018], the canonical correlation vectors described by CCA effectively capture correlated gene modules that are present in both datasets, representing genes that define a shared biological state....
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...We also tested the following existing integration methods on the same holdout datasets: Seurat v2 [Butler et al., 2018], mnnCorrect [Haghverdi et al....
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...Canonical correlation vectors are calculated as described previously [Butler et al., 2018]....
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...While we have previously suggested using saturation or statistical-resampling based approaches to estimate dataset dimensionality [Butler et al., 2018], a robust fully unsupervised procedure to identify this value remains a fundamental challenge in the analysis of high-dimensional data....
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References
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