Computational Biology
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[Study Note] Techniques of scRNA-seq: From Counts to Biological Inference
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A connected guide to preprocessing, variance stabilization, embeddings, annotation, differential analysis, trajectories, and communication.
[Paper Review] muscat: Differential States Across Biological Samples
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Why the sample is the unit of replication, how pseudobulk works, and what different differential-state methods test.
[Paper Review] MAGIC: Diffusion on a Cell Similarity Graph
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A step-by-step explanation of affinity kernels, Markov transitions, diffusion, and the limits of expression smoothing.
[Paper Review] GLUE: Integrating Unpaired Single-Cell Multi-Omics
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Cell embeddings, feature embeddings, and guidance graphs for integrating assays measured in different cells.