LRBase × scTensorで細胞間コミュニケーションの検出
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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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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 gallery by DBCLS is Licensed under a Creative Commons 2.1 (c)
- 9. Pavilicev M, 2017 Ramilowski J A, 2015 Li L, 2017 Skelly D A, 2018
- 10. Togo picture gallery by DBCLS is Licensed under a Creative Commons 2.1 (c)
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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.)
- 26. library(scTensor) library(SingleCellExperiment) library(LRBase.Hsa.eg.db) data(“GermMale”) # Data matrix (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
- 34. 1/4
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- 39. 3/4 Gusev A. et. al., 2016Sun S. et. al., 2018
- 40. 4/4
- 41. 4/4 Butler A et. al., 2018Brown B C et. al., 2018
- 43. = Raquel Urtasun, 2008Laurens, 2008 Graph PCA, Bo Jiang, 2013
- 44. PCA: 1 X
- 48. CMF: n Marinka Zitnik, 2016
- 49. CMTF: n Ermis B, 2012 Suleiman A Khan, 2016 Evirm Acar, 2011