scTensor-package {scTensor} | R Documentation

## Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

### Description

The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.

### Details

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.

### Author(s)

NA

Maintainer: NA

### See Also

`GermMale`,`labelGermMale`, `tsneGermMale`,`cellCellSetting`, `cellCellDecomp`,`cellCellReport`

### Examples

    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")
    }

[Package scTensor version 1.2.1 Index]