scTensor-package {scTensor} | R Documentation |
The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.
The DESCRIPTION file:
Package: | scTensor |
Type: | Package |
Title: | Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition |
Version: | 1.2.1 |
Authors@R: | c(person("Koki", "Tsuyuzaki", role = c("aut", "cre"), email = "k.t.the-answer@hotmail.co.jp"), person("Kozo", "Nishida", role = "aut", email = "kozo.nishida@gmail.com")) |
Depends: | R (>= 3.5.0) |
Imports: | methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices, graphics, stats, utils, outliers, Category, meshr, GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork |
Suggests: | testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db, MeSH.Mmu.eg.db, LRBaseDbi, Seurat, Homo.sapiens |
Description: | The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor. |
License: | Artistic-2.0 |
biocViews: | DimensionReduction, SingleCell, Software, GeneExpression |
VignetteBuilder: | knitr |
git_url: | https://git.bioconductor.org/packages/scTensor |
git_branch: | RELEASE_3_10 |
git_last_commit: | c4b8069 |
git_last_commit_date: | 2019-11-08 |
Date/Publication: | 2019-11-09 |
Author: | Koki Tsuyuzaki [aut, cre], Kozo Nishida [aut] |
Maintainer: | Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp> |
Index of help topics:
CCSParams-class Class "CCSParams" GermMale The matrix which is used as test data of scTensor. cellCellDecomp Performing scTensor cellCellRanks Rank estimation of the CCI-tensor cellCellReport HTML report of the result of scTensor cellCellSetting Parameter setting for scTensor cellCellSimulate Parameter Simulate for scTensor convertToNCBIGeneID ID conversion function to create the input matrix for scTensor getParam Get a parameter labelGermMale The vector contains the celltype information and color scheme of GermMale m The gene-wise mean vector of Quartz-Seq data. newCCSParams New Params scTensor-package Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition setParam Set a parameter tsneGermMale The result of Rtsne against GermMale v The gene-wise variance vector of Quartz-Seq data.
NA
Maintainer: NA
GermMale
,labelGermMale
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tsneGermMale
,cellCellSetting
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cellCellDecomp
,cellCellReport
if(interactive()){ # Package Loading library(SingleCellExperiment) library(LRBase.Hsa.eg.db) # Data Loading data(GermMale) data(labelGermMale) data(tsneGermMale) # SingleCellExperiment-class sce <- SingleCellExperiment(assays = list(counts = GermMale)) reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y) # Setting cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale)) # Decomposition cellCellDecomp(sce, ranks=c(4,4,5)) # Report tmp <- tempdir() cellCellReport(sce, reducedDimNames="TSNE", out.dir=tmp, html.open = TRUE, title="Cell-cell interaction within Germline, Male, GSE86146", author="Koki Tsuyuzaki", thr=5) }else{ ls("package:scTensor") }