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")

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