scTensor

DOI: 10.18129/B9.bioc.scTensor  

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

Bioconductor version: Release (3.16)

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	2.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 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
Links To Me
Build Report

Package Archives

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

Source Package	scTensor_2.8.0.tar.gz
Windows Binary	scTensor_2.8.0.zip
macOS Binary (x86_64)	scTensor_2.8.0.tgz
macOS Binary (arm64)	scTensor_2.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scTensor
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scTensor
Bioc Package Browser	https://code.bioconductor.org/browse/scTensor/
Package Short Url	https://bioconductor.org/packages/scTensor/
Package Downloads Report	Download Stats