Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
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Title
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
Authors
Keywords
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Journal
NATURE METHODS
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2022-05-17
DOI
10.1038/s41592-022-01480-9
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- (2021) Marc Elosua-Bayes et al. NUCLEIC ACIDS RESEARCH
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- (2021) Yinlei Hu et al. BRIEFINGS IN BIOINFORMATICS
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- (2019) Sonja Nowotschin et al. NATURE
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- (2019) Soufiane Mourragui et al. BIOINFORMATICS
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- (2019) Tim Stuart et al. CELL
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- (2019) Joshua D. Welch et al. CELL
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