非負値テンソル分解を用いた細胞間コミュニケーション検出
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The document describes performing dimensionality reduction, cell-cell interaction analysis, and reporting on single-cell RNA-seq data from a study of germline cells in male samples. It loads the gene expression, dimensionality reduced data, and cell type labels into a SingleCellExperiment object. Cell-cell interaction ranks are calculated and used for decomposition. A report is generated on the cell-cell interactions within each cell type at a threshold of 80%.
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非負値テンソル分解を用いた細胞間コミュニケーション検出
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- 22. 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) cellCellReport(sce, reducedDimNames="TSNE", out.dir=tmp, title="Cell-cell interaction within Germline, Male, GSE86146", author="Koki Tsuyuzaki", thr=80)