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LRBase × scTensorで細胞間コミュニケーションの検出
This document describes a method for analyzing cell-cell interactions within single-cell RNA-seq data using tensor decomposition. It references several papers on tensor decomposition and single-cell analysis methods. The document also includes code to load a sample single-cell dataset, perform tensor decomposition on it, and generate reports of the results.
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References to Chen S (2015) and others with Creative Commons licensing for Togo picture gallery.
References to Chen S (2015) and others with Creative Commons licensing for Togo picture gallery.
Utilizing mathematical symbols to denote relationships with variables and parameters X, u1', v1', and λ.
Citing the ongoing preparation of research works by Tsuyuzaki K. et al. (2019) across four items.
Utilizing libraries and data matrices for analyzing cell types with specific scripts for data processing.
Citations related to previous research by Tsuyuzaki K. et al. for the years 2018.
Citations related to previous research by Tsuyuzaki K. et al. for the years 2018.
Presentation of research citations split into sections, referencing multiple studies over four parts.
Discusses various statistical techniques like PCA, PLS, CCA, and CMF with respective citations.
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LRBase × scTensorで細胞間コミュニケーションの検出
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- 7. Togo picture galleryby DBCLS is Licensed under a Creative Commons 2.1 (c)
- 9. Pavilicev M, 2017 RamilowskiJ A, 2015 Li L, 2017 Skelly D A, 2018
- 10. Togo picture galleryby DBCLS is Licensed under a Creative Commons 2.1 (c)
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- 14. X X1 X2X3 ^ ^ ^
- 15. X u1'◦v1' u2'◦v2' u3'◦v3' X1X2 X3 ^ ^ ^
- 16. X u1'◦v1' u2'◦v2' u3'◦v3' u1◦v1u2◦v2 u3◦v3 X1 X2 X3 ^ ^ ^ λ1 λ2 λ3
- 17. X u1'◦v1' u2'◦v2' u3'◦v3' u1◦v1u2◦v2 u3◦v3 UΛVT X1 X2 X3 ^ ^ ^ λ1 λ2 λ3
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- 21. 1 Tsuyuzaki K. et.al., 2019 (in prep.)
- 22. 2 Tsuyuzaki K. et.al., 2019 (in prep.)
- 23. 3 Tsuyuzaki K. et.al., 2019 (in prep.)
- 24. 4 Tsuyuzaki K. et.al., 2019 (in prep.)
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- 26. library(scTensor) library(SingleCellExperiment) library(LRBase.Hsa.eg.db) data(“GermMale”) # Datamatrix (486genes × 852cells, 7class, 3.5MB) data(“tsneGermMale”) # The result of Rtsne (21kb) data(“labelGermMale”) # Celltype label (15kb) sce <- SingleCellExperiment(assays = list(counts = GermMale)) reducedDims(sce) <- SimpleList(TSNE = tsneGermMale$Y) cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale)) rks <- cellCellRanks(sce) cellCellDecomp(sce, ranks=rks$selected) cellCellReport(sce, reducedDimNames="TSNE", out.dir=tmp, title="Cell-cell interaction within Germline, Male, GSE86146", author="Koki Tsuyuzaki", thr=80)
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- 33. Tsuyuzaki K. et.al., 2018
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- 35. 1/4 Himmelstein, D Set al., 2017
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- 37. 2/4 Cichonska, A etal., 2015
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- 39. 3/4 Gusev A. et.al., 2016Sun S. et. al., 2018
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- 41. 4/4 Butler A et.al., 2018Brown B C et. al., 2018
- 43. = Raquel Urtasun, 2008Laurens,2008 Graph PCA, Bo Jiang, 2013
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- 49. CMTF: n Ermis B,2012 Suleiman A Khan, 2016 Evirm Acar, 2011
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