There is more than just tSNE and UMAP in Single Cell Dimensional Reduction. In this post I will check Phate.

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t-SNE & UMAP dimensional reduction for single cell data. How to choose between them?

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Pseudotime trajectories and RNA velocity are computational approaches to analyze single cell dynamical process but, do they tell the same history?

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How to use scVelo to explore gene expression dynamics and differentiation

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Using Slingshot to calculate single cell trajectories

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PCA is the first step of single cell data analysis, but how many PCs should you use?

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See ENACT, a complete end-to-end pipeline that includes Visium HD Cell Segmentation and Cell type annotation, in action.

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Moving beyond nuclei segmentation, this post explores Bin2Cell for full cell segmentation in Visium HD spatial data.

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Nuclei segmentation from Visium HD data

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Explore SingleCellExperiment in R! Master data structures & workflows to handle single-cell RNA-seq data effectively in your research projects.

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