scTensor

DOI: 10.18129/B9.bioc.scTensor    

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

Bioconductor version: Release (3.15)

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

Author: Koki Tsuyuzaki [aut, cre], Kozo Nishida [aut]

Maintainer: Koki Tsuyuzaki <k.t.the-answer at hotmail.co.jp>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scTensor")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scTensor")

 

HTML	R Script	scTensor
HTML	R Script	scTensor: 1. Data format and ID conversion
HTML	R Script	scTensor: 2. Interpretation of HTML report
HTML	R Script	scTensor: 3. Simulation of CCI
HTML	R Script	scTensor: 4. Reanalysis of the results of scTensor
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, GeneExpression, SingleCell, Software
Version	2.6.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 years)
License	Artistic-2.0
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
LinkingTo
Suggests	testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scTensor_2.6.0.tar.gz
Windows Binary	scTensor_2.6.0.zip
macOS Binary (x86_64)	scTensor_2.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scTensor
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scTensor
Package Short Url	https://bioconductor.org/packages/scTensor/
Package Downloads Report	Download Stats