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: | 2.4.1
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 (>= 4.1.0)
Imports: | methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2
Suggests: | testthat, LRBaseDbi, Seurat, scTGIF, 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_14
git_last_commit: | e0462fa
git_last_commit_date: | 2021-12-16
Date/Publication: | 2021-12-19
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
    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

    ls("package:scTensor")

[Package scTensor version 2.4.1 Index]