scTensor

DOI: 10.18129/B9.bioc.scTensor    

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

Bioconductor version: Release (3.14)

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>

Citation (from within R, enter citation("scTensor")):

Installation

To install this package, start R (version "4.1") 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 2.4.1
In Bioconductor since BioC 3.9 (R-3.6) (3 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_2.4.1.tar.gz
Windows Binary scTensor_2.4.1.zip
macOS 10.13 (High Sierra) scTensor_2.4.1.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
Old Source Packages for BioC 3.14 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: