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Distinguish genes that show true biological variation
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Significant technical noise is present
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Hypothesis testing based on identification of variation that exceeds empirical estimations of technical noise [11]
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What genes vary among physiologically distinct cells of seemingly homogenous tissues?
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Profiles have no replicates and exhibit zero-biased expression distribution, so traditional statistical methods are inappropriate
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Model-driven deconvolution of biological variation using estimations of technical noise [20]
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Identify transcriptional signature of rare cell types
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Linear dimensionality reduction can obscure close relationships and produce misleading clusters
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Non-linear t-SNE to minimize joint probability distribution distance and draw similar cells together [29]
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What is the transcriptional profile of root initials?
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Clustering methods might miss small sets of cells
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backSPIN to impose an order and partition data [31, 32]
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Find subsets of cells with a unique environmental response
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Separation of a continuous cell expression space into types is subjective
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RaceID to identify new cell types by detecting a significant number of biological gene outliers [30]
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What is the early response of pathogen-susceptible vs. pathogen-resistant cells of the leaf epidermis?
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Assemble dissociated cells into a developmental sequence
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Missing data-points exist owing to false negatives and misleading false positives
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De novo trajectory reconstruction to order cells using Monocle [39] or diffusion-like dynamics [40]
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What is the ordered profile of specific cell types from initial to differentiated cells?
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Variation in individual plants can create artificial groupings
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Seurat to map cells using a priori data and imputation of missing data-points [41]
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ICI to map cells to known reference types using many markers [12, 38]
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Follow identity transitions during wound repair or in vitro regeneration
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Detecting transitional and multiple identities must be robust in single-cell data with many false positives and false negatives
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ICI to classify cells using a priori knowledge of identity markers for detecting mixed or diminished cell identity [12, 38]
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Do plant cells follow a course of de- or trans- differentiation during regeneration?
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