SpatialDE: identification of spatially variable genes

Svensson, Valentine, Teichmann, Sarah A, Stegle, Oliver·2018·Nature Methods
DOI 10.1038/nmeth.4636

Cited by (710)

Items 301–400 of 710

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  6. Identification of spatially variable genes with graph cuts
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  8. The cellular and molecular landscape of hypothalamic patterning and differentiation
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  15. Emerging Roles of Spatial Transcriptomics in Liver Research
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  16. Transfer learning of multicellular organization via single-cell and spatial transcriptomics
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  17. High-precision cell-type mapping and annotation of single-cell spatial transcriptomics with STAMapper
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  21. Alignment of spatial genomics and histology data using deep Gaussian processes
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  22. An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology
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  30. Spatial resolved transcriptomics: Computational insights into gene transcription across tissue and organ architecture in diverse applications
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  31. Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas
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  80. An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
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  81. Metric learning enables synthesis of heterogeneous single-cell modalities
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  92. Comparative Analysis of Packages and Algorithms for the Analysis of Spatially Resolved Transcriptomics Data
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  93. Representing and extracting knowledge from single-cell data
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  95. SpatialOne: end-to-end analysis of visium data at scale
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  96. Multiscale Dissection of Spatial Heterogeneity by Integrating Multi‐Slice Spatial and Single‐Cell Transcriptomics
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  97. SpaceBF: spatial coexpression analysis using Bayesian fused approaches in spatial omics datasets
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  98. SpaceWalker enables interactive gradient exploration for spatial transcriptomics data
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