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 (NTD) 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: 1.0.7
Date: 2019-07-15
Authors@R: person("Koki", "Tsuyuzaki", role = c("aut", "cre"), email = "k.t.the-answer@hotmail.co.jp")
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
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 (NTD) of nnTensor.
License: Artistic-2.0
biocViews: DimensionReduction, SingleCell
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/scTensor
git_branch: RELEASE_3_9
git_last_commit: 4e7a527
git_last_commit_date: 2019-07-15
Date/Publication: 2019-07-15
Author: Koki Tsuyuzaki [aut, cre]
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 1.0.7 Index]