scTensor-package {scTensor}R Documentation

Detection of cell-cell interaction within single-cell RNA-Seq data

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 within single-cell RNA-Seq data
Version: 1.0.0
Date: 2018-11-06
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, biomaRt, 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
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: 593b9b6
git_last_commit_date: 2019-05-02
Date/Publication: 2019-05-02
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>

Index of help topics:

.m                      The gene-wise mean vector of Quartz-Seq data.
.v                      The gene-wise variance vector of Quartz-Seq
                        data.
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
getParam                Get a parameter
labelGermMale           The vector contains the celltype information
                        and color scheme of GermMale
newCCSParams            New Params
scTensor-package        Detection of cell-cell interaction within
                        single-cell RNA-Seq data
setParam                Set a parameter
tsneGermMale            The result of Rtsne against GermMale

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 1.0.0 Index]