2019
DOI: 10.1038/s41467-019-09670-4
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Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

Abstract: Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex b… Show more

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Cited by 236 publications
(250 citation statements)
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References 53 publications
(42 reference statements)
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“…A common practice for clustering and trajectory finding methods is to preprocess the data by selecting highly variable genes and performing dimension reduction using principal component analysis (PCA) 19 or t-Distributed Stochastic Neighbor Embedding (tSNE) 20 . Examples include Seurat 6,13,21 , pcaReduce 22 , MNN batch-effectcorrection 23 , RaceID3 24 , TSCAN 25 , STREAM 26 , and many others. There are also imputation methods designed to explicitly remove dropouts.…”
mentioning
confidence: 99%
“…A common practice for clustering and trajectory finding methods is to preprocess the data by selecting highly variable genes and performing dimension reduction using principal component analysis (PCA) 19 or t-Distributed Stochastic Neighbor Embedding (tSNE) 20 . Examples include Seurat 6,13,21 , pcaReduce 22 , MNN batch-effectcorrection 23 , RaceID3 24 , TSCAN 25 , STREAM 26 , and many others. There are also imputation methods designed to explicitly remove dropouts.…”
mentioning
confidence: 99%
“…Indeed, the framework may also be applicable to, e.g., downstream analysis of chromatin accessibility trajectories in scATAC-seq datasets (e.g. Chen et al [2019]) or bulk RNA-seq time-course studies.…”
Section: Discussionmentioning
confidence: 99%
“…At a proteomic level, researchers have identified proteins in the brain which are associated with the cognitive trajectory in the elderly (11). Finally, the evolution of single-cell sequencing has allowed the evaluation of these different layers in greater detail (12). The analysis of omics data has advanced the understanding of human diseases, but it is important to remember that these studies represent only one layer of a more complex system.…”
Section: Integrative Biology Approaches Applied To Human Diseases Intmentioning
confidence: 99%
“…Clustering analyses in scRNA-seq data can be very useful and informative, but they are not always able to describe dynamic biological processes involved in transitions between different states, such as cellular proliferation and maturation (12). Such events can be computationally modeled through the reconstruction of the cell trajectory and pseudotime estimation (53).…”
Section: Tools For the Analysis Of Single-layer High-throughput Datamentioning
confidence: 99%