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Similar to 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
Similar to 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 (18)
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
- 16. χ
A(1)
A(2)
A(3)
S
χ(1,1,1)
χ
χ
S(1,1,1)
S(1,1,2)
S(J1,J2,J3)
(1,1,2)
(J1,J2,J3)
^
^
^
- 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)